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Supplemental Methods - Epigenenomics of Sample_Group in Heart Failure |
Mark E. Pepin |
31 December, 2021 |
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Code Author: Mark E. Pepin, MD, PhD, MS Contact: [email protected]{.email} Institution: Heidelberg University Hospital Location: 669 Neuenheimer Feld, Institute for Experimental Cardiology, 69120 Heidelberg, Germany
Define the parameters used, along with the conditions required for the current analysis. This segment must be modified for each analysis performed.
##Set the experimental conditions [MUST DO THIS MANUALLY]
Run_tS<-Sys.time()
TREATMENT=c("CON", "DCM")
CELL=c("iPSC")
STATISTIC = 0.05 #P statistic threshold used in this combination.
VARIABLE = TREATMENT
COMPARISON= paste0(CELL[1], "_",VARIABLE[2], "_vs_", VARIABLE[1])
# Candidate Gene Selection (RNA-sequencing) EDIT THIS LIST BASED ON INTERESTS.
GENES=c("LEP", "ADIPOQ", "PLIN1")
VAR1="Treatment"
VAR2="Diabetes"
# Single Bar Graph
library(dplyr)
my_comparisons <- list( c("CON", "DCM")) # Comparisons to make
## Create color based on Genotype
ann_colors = list(Treatment = c(DCM="darkgray", CON = "darkcyan"))
TreatmentColors<-ann_colors$Treatment
ann_colorTable<-as.data.frame(ann_colors)
ann_colGroup<-subset(ann_colorTable, rownames(ann_colorTable) %in% TREATMENT)
ann_colListGroup<-list(ann_colors$Treatment)
ann_colGroupVec<-ann_colGroup$Treatment
names(ann_colGroupVec)<-as.factor(rownames(ann_colGroup))
GROUP_colors<-list(ann_colGroupVec=ann_colGroupVec)
# Create Output Folder Structure
ifelse(!dir.exists(file.path(paste0("../2_Output/"))), dir.create(file.path(paste0("../2_Output/"))), FALSE)## [1] FALSE
ifelse(!dir.exists(file.path(paste0("../2_Output/", COMPARISON))), dir.create(file.path(paste0("../2_Output/", COMPARISON))), FALSE)## [1] FALSE
if (!require("pacman")) install.packages("pacman")
pacman::p_load(dplyr, Hmisc, openxlsx, corrplot, RColorBrewer, kableExtra, ggplot2, gridExtra, ggpubr, ggsignif, DESeq2, data.table, GenomicFeatures, biomaRt, Haplin, pheatmap, calibrate, ggrepel, tidyr, gtools)library(minfi)
library(limma)
library(shinyMethyl)
library(dplyr)
library(IlluminaHumanMethylation450kmanifest)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(RColorBrewer)
#########Part 1: Importing the Data
#Parameters
##Get the array annotation
annoM450k<-getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
annoM450k<-dplyr::select(as.data.frame(annoM450k), Name, chr, pos, Relation_to_Island, UCSC_RefGene_Name, UCSC_RefGene_Accession, UCSC_RefGene_Group, Regulatory_Feature_Group)
#Import the sample sheet
targets<-read.metharray.sheet(base="../1_Input/IDAT", pattern=".csv")## [1] "../1_Input/IDAT/SampleSheet.csv"
#Import the annotation file
AnnoTargets<-targets
targets$ID <- paste(targets$Sample_Group,targets$Sample_Name,sep=".")
targets$Sample_Well<-AnnoTargets$Sample_Well
targets$Sample_Plate<-AnnoTargets$Sample_Plate
targets$Sample_Group<-AnnoTargets$Sample_Group
targets$Sample_Group<-factor(targets$Sample_Group, levels = c("CON", "DCM"))
targets$Sex<-AnnoTargets$Sex
targets$Outcome<-AnnoTargets$Outcome
targets$Conc<-AnnoTargets$Conc
targets$Col_ID<-AnnoTargets$Col_ID
targets$Tissue<-AnnoTargets$Tissue
targets<-targets %>% filter(Tissue %in% CELL)
#Import the array data from input directory (red and green .idat files)
RGSet<-read.metharray.exp(base = "../1_Input/IDAT", targets = targets, verbose = TRUE)
sampleNames(RGSet)<-targets$Sample_Name
##Quality Control
#First step is to identify CpGs that failed to identify methylated positions (defined by expression intensity that reflects background levels)
detP<-detectionP(RGSet)
PLOT.COL <- brewer.pal(8,"Dark2")
##Detection P-value Plot
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_detectionP.pdf"))
par(mfrow=c(1,1))
barplot(colMeans(detP), col=PLOT.COL[factor(targets$Sample_Group)],
cex.names=0.8, ylim=c(0,0.005), ylab="Mean detection p-values")
abline(h=0.05,col="red")
legend("topleft", legend=levels(factor(targets$Sample_Group)), fill=PLOT.COL,
bg="white")
dev.off()## quartz_off_screen
## 2
## Filter RGSet by detection P-value
keep <- colMeans(detP) < 0.05
RGSet <- RGSet[,keep]
RGSet## class: RGChannelSet
## dim: 622399 24
## metadata(0):
## assays(2): Green Red
## rownames(622399): 10600313 10600322 ... 74810490 74810492
## rowData names(0):
## colnames(24): A1_cells_bo A2_cells_bo ... C9_cells_co C10_cells_co
## colData names(17): Sample_Name Sample_Well ... ID filenames
## Annotation
## array: IlluminaHumanMethylation450k
## annotation: ilmn12.hg19
##QC Report
qcReport(RGSet, sampNames=targets$ID, sampGroups=targets$Sample_Group, pdf="qcReport.pdf")## quartz_off_screen
## 2
#
par(mfrow=c(1,1))
barplot(colMeans(detP), col=PLOT.COL[factor(targets$Sample_Group)], las=2,
cex.names=0.8, ylim=c(0,0.005), ylab="Mean detection p-values")
abline(h=0.05,col="red")
legend("topleft", legend=levels(factor(targets$Sample_Group)), fill=PLOT.COL,
bg="white")
# #Determine the fraction of "failed" CpG probes (those which failed to identify a methylated CpG)
# colMeans(failed)
#Convert R/G to Methylated/Unmethylated in an object of class MethylSet
MSet<-preprocessRaw(RGSet)
#QC data
qc<-getQC(MSet)
plotQC(qc)
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_QC.Methyl.pdf"))
plotQC(qc)
dev.off()## quartz_off_screen
## 2
##Density plot
# densityPlot(RGSet, sampGroups = targets$Sample_Group, main= "Beta", xlab = "Beta")
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_densityPlot.pdf"))
densityPlot(RGSet, sampGroups = targets$Sample_Group, main= "Beta", xlab = "Beta")
dev.off()## quartz_off_screen
## 2
densityBeanPlot(RGSet, sampGroups = targets$Sample_Group)
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_BeanPlot.pdf"))
densityBeanPlot(RGSet, sampGroups = targets$Sample_Group)
dev.off()## quartz_off_screen
## 2
qcReport(RGSet, pdf= paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_qcReport.pdf"))## quartz_off_screen
## 2
# #Convert to a shinyMethyl dataset (nice summary of the quality control)
# summarized.data <- shinySummarize(RGSet)
# runShinyMethyl(summarized.data)
gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE)
beta.all<-getBeta(RGSet)
write.csv(beta.all, "../1_Input/EPIC.betaValues.csv")par(mfrow=c(1,1))
barplot(colMeans(detP), col=PLOT.COL[factor(targets$Sample_Group)], las=2,
cex.names=0.8, ylim=c(0,0.005), ylab="Mean detection p-values")
abline(h=0.05,col="red")
legend("topleft", legend=levels(factor(targets$Sample_Group)), fill=PLOT.COL,
bg="white")
Because such a robust racial signature in cardiac DNA methylation was seen in the pilot analysis, we reproduced the unsupervised method in the larger cohort. This time, we continue to see a distinct racial difference. Furthermore, we found that this racially-determined clustering persisted to among the 500,000 most-variable CpG probes in the EPIC array.
#Plot Features of the PCA
library(dplyr)
library(plotly)
##Import the data to be used for PCA
Index_PCA<-targets
rownames(Index_PCA)<-Index_PCA$Sample_Name
PCA_data<-as.data.frame(getM(gRatioSet.quantile))
#transpose the dataset (required for PCA)
data.pca<-t(PCA_data)
data.pca<-as.data.frame(data.pca)
##merge the file
data.pca_Final<-merge(Index_PCA, data.pca, by=0)
rownames(data.pca_Final)<-data.pca_Final$Row.names
pca.comp<-prcomp(data.pca_Final[,(ncol(Index_PCA)+2):ncol(data.pca_Final)])
pcaCharts=function(x) {
x.var <- x$sdev ^ 2
x.pvar <- x.var/sum(x.var)
par(mfrow=c(2,2))
plot(x.pvar,xlab="Principal component",
ylab="Proportion of variance", ylim=c(0,1), type='b')
plot(cumsum(x.pvar),xlab="Principal component",
ylab="Cumulative Proportion of variance",
ylim=c(0,1),
type='b')
screeplot(x)
screeplot(x,type="l")
par(mfrow=c(1,1))
}
pcaCharts(pca.comp)
png(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_PCA.Charts.png"))
pcaCharts(pca.comp)
dev.off()## quartz_off_screen
## 2
From the previous calculations, it is seens that only 2 principal components are necessary (accounting for >80% cumulative variance). Nonetheless, below is a 3-D PCA to ensure that all groups are characterize to higher-degree of stringency. Nevertheless, a racial difference could not be appreciated.
##Create a 3D-PCA for Inspection
library(plotly)
##Index
Index_PCA<-targets
rownames(Index_PCA)<-Index_PCA$Sample_Name
PCs<-merge(pca.comp$x, Index_PCA, by=0)
rownames(PCs)<-PCs$Row.names
PCs$Group <- as.factor(PCs$Sample_Group)
fig <- plot_ly(PCs, x = ~PC1, y = ~PC2, z = ~PC3, color = ~Sample_Group, text = ~paste('Sample_Name:', Sample_Name, '<br>Tissue:', Tissue, '<br>Outcome:', Outcome, '<br>Sex:', Sex))
fig <- fig %>% add_markers()
fig <- fig %>% layout(scene = list(xaxis = list(title = 'PC1'),
yaxis = list(title = 'PC2'),
zaxis = list(title = 'PC3')))
fig<div id="htmlwidget-0ed3cff61cab74c0c287" style="width:672px;height:480px;" class="plotly html-widget"></div>
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Owing to the apparent separation by patient Sample_Group, we chose to identify the CpG sites responsible for a Sample_Group-based epigenomic difference.
#Quantification and Differential Expression Analysis
RGSet<-read.metharray.exp(base = "../1_Input/IDAT", targets = targets, verbose = TRUE)
# sampleNames(RGSet)<-targets$Sample_Name
GRset.funnorm <- preprocessFunnorm(RGSet)
beta <- getBeta(GRset.funnorm)
M<-getM(GRset.funnorm)
Condition <- pData(GRset.funnorm)$Sample_Group
dmp <- dmpFinder(beta, pheno = Condition , type = "categorical")
DMPs<-merge(dmp, annoM450k, by= 0)
DMPs<-as.data.frame(DMPs)
rownames(DMPs)<-DMPs$Row.names
DMPs<-DMPs %>% dplyr::select(-Row.names)
#create an beta table
beta.table<-as.data.frame(t(beta))
beta.table$Col_ID<-rownames(beta.table)
beta_named<-merge(beta.table, targets, by = "Col_ID")
rownames(beta_named)<-beta_named$Sample_Name
beta_named<-beta_named %>% dplyr::select(-names(targets)) %>% t()
write.csv(beta_named, paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_beta.table.csv"))
#Add beta values to statistics
Results_dmp<-merge(DMPs, beta_named, by = 0)
#Calculate Average CpG Methylation by Sample_Group
library(dplyr)
library(matrixStats)
Results<-Results_dmp %>% replace(is.na(.), 0) %>% dplyr::mutate(
DCM_SD = rowSds(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="DCM"]])),
DCM_Mean = rowMeans(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="DCM"]])),
CON_SD = rowSds(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="CON"]])),
CON_Mean = rowMeans(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="CON"]])),
Methylation.Diff=(DCM_Mean-CON_Mean)*100)
rownames(Results)<-Results$Row.names
Results_dmp_p05<-filter(Results, pval<0.05)
Results_dmp_q05<-filter(Results, qval<0.05)
#########################################
#Identify Promoter-associated CpG Islands
library(tidyr)
PromCGI<-dplyr::filter(Results_dmp_p05, grepl("Island", Relation_to_Island), grepl("TSS", UCSC_RefGene_Group))
#Separate Gene Names into unique rows
PromCGI_sep<-PromCGI %>% mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>% unnest(UCSC_RefGene_Name) %>% distinct()
#Save a copy of the countData
library(openxlsx)
wb_countData<-createWorkbook()
addWorksheet(wb_countData, "Unfiltered")
writeData(wb_countData, "Unfiltered", Results, startCol = 1)
addWorksheet(wb_countData, "P_0.05")
writeData(wb_countData, "P_0.05", Results_dmp_p05, startCol = 1)
addWorksheet(wb_countData, "Q_0.05")
writeData(wb_countData, "Q_0.05", Results_dmp_q05, startCol = 1)
addWorksheet(wb_countData, "Promoter.CGI")
writeData(wb_countData, "Promoter.CGI", PromCGI_sep, startCol = 1)
saveWorkbook(wb_countData, file = paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_DMPs.xlsx"), overwrite = TRUE)The following figure illustrates the enrichment of differential methylation with respect to CpG-based and genomic annotations.
library(plotly)
library(dplyr)
library(tidyr)
library(stringr)
library(reshape2)
library(readxl)
library(kableExtra)
library(ComplexHeatmap)
library(openxlsx)
##Create a regional annotation matrix of the m450k array
Region_epic<-Results_dmp %>%
dplyr::select(Row.names, UCSC_RefGene_Group, Relation_to_Island)
Stage1<-Region_epic %>%
mutate(UCSC_RefGene_Group = strsplit(as.character(UCSC_RefGene_Group), ";")) %>%
unnest(UCSC_RefGene_Group)
Stage2<-Stage1 %>%
mutate(Relation_to_Island = strsplit(as.character(Relation_to_Island), ";")) %>%
unnest(Relation_to_Island)
Stage3<-distinct(Stage2)
Regional.Groups<-dplyr::group_by_(Stage3, "UCSC_RefGene_Group", "Relation_to_Island") %>%
tally()
Region.matrix<-Regional.Groups %>%
spread(Relation_to_Island, n)
Region.matrix<-Region.matrix %>%
dplyr::select(UCSC_RefGene_Group, OpenSea, N_Shelf, N_Shore, Island, S_Shore, S_Shelf)
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Region.matrix<-Region.matrix[c("TSS1500", "TSS200", "5'UTR", "1stExon", "Body", "3'UTR"),]
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Contour_3D_epic<-Region.matrix[,-1]
rownames(Contour_3D_epic)<-Region.matrix$UCSC_RefGene_Group
write.xlsx(Contour_3D_epic, "../2_Output/Contour.3D_EPIC.xlsx", overwrite = TRUE)
##Create a regional annotation matrix of differentially-methylated positions
Region_p05<-Results_dmp_p05 %>% dplyr::select(Row.names, UCSC_RefGene_Group, Relation_to_Island)
Stage1<-Region_p05 %>% mutate(UCSC_RefGene_Group = strsplit(as.character(UCSC_RefGene_Group), ";")) %>% unnest(UCSC_RefGene_Group)
Stage2<-Stage1 %>% mutate(Relation_to_Island = strsplit(as.character(Relation_to_Island), ";")) %>% unnest(Relation_to_Island)
Stage3<-distinct(Stage2)
Regional.Groups<-dplyr::group_by_(Stage3, "UCSC_RefGene_Group", "Relation_to_Island") %>% tally()
Region.matrix<-Regional.Groups %>% spread(Relation_to_Island, n)
Region.matrix<-Region.matrix %>% dplyr::select(UCSC_RefGene_Group, OpenSea, N_Shelf, N_Shore, Island, S_Shore, S_Shelf)
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Region.matrix<-Region.matrix[c("TSS1500", "TSS200", "5'UTR", "1stExon", "Body", "3'UTR"),]
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Contour_3D<-Region.matrix[,-1]
rownames(Contour_3D)<-Region.matrix$UCSC_RefGene_Group
write.csv(Contour_3D, "../2_Output/Contour.3D_DMPs.p05.csv")
### Identify DMP Enrichment (IMPORTANT)
Enrichment_Region<-Contour_3D/Contour_3D_epic
Promoter_enr<-Enrichment_Region[rownames(Enrichment_Region)=="TSS200",] + Enrichment_Region[rownames(Enrichment_Region)=="TSS1500",]
rownames(Promoter_enr)<-"Promoter"
Enrichment_Region<-Enrichment_Region %>%
filter(!grepl("TSS", rownames(Enrichment_Region))) %>%
rbind(Promoter_enr, .) %>%
data.matrix()
paletteLength<-100
myColor <- colorRampPalette(c("dodgerblue4", "white", "brown4"))(paletteLength)
pheatmap(Enrichment_Region, color = myColor, cluster_rows = FALSE, cluster_cols = FALSE, filename = paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_DMP.Distribution.pdf"))
write.csv(Enrichment_Region, "DCM_vs_CON.csv")
##Make a Table of the CpG Methylation Distribution
Enrichment_Region %>% kable( align="c", booktabs=T,
caption="Methylation Distribution") %>%
kable_styling(latex_options=c("striped", "condensed", "repeat_header"))| OpenSea | N_Shelf | N_Shore | Island | S_Shore | S_Shelf | |
|---|---|---|---|---|---|---|
| Promoter | 0.1164621 | 0.1029990 | 0.1242210 | 0.1460420 | 0.1156378 | 0.1037933 |
| 5'UTR | 0.0530359 | 0.0622389 | 0.0569429 | 0.0741839 | 0.0573959 | 0.0576832 |
| 1stExon | 0.0588488 | 0.0489130 | 0.0623833 | 0.0746424 | 0.0625000 | 0.0370370 |
| Body | 0.0523911 | 0.0493794 | 0.0510093 | 0.0633285 | 0.0507863 | 0.0473963 |
| 3'UTR | 0.0485610 | 0.0415879 | 0.0554833 | 0.0638298 | 0.0563931 | 0.0479303 |
write.xlsx(Enrichment_Region, paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_DMP.Enrichment_3D.xlsx"), overwrite = T)
color <- colorRampPalette(c("grey", "orange", "red"))
t <- list(
family = "times",
size = 16,
color = "black")
x_axis<-list(title = 'CpG Region',
type="category",
zeroline=TRUE,
showline=TRUE,
zerolinewidth = 4,
zerolinecolor="darkgrey",
linecolor="darkgrey",
linewidth=4,
titlefont=t,
tickfont=t)
y_axis<-list(title = 'Gene Region',
type="category",
zeroline=TRUE,
showline=TRUE,
zerolinewidth = 4,
zerolinecolor="darkgrey",
linecolor="darkgrey",
linewidth=4,
titlefont=t,
tickfont=t)
z_axis<-list(title = 'Number of DMPs',
zerolinewidth = 4,
zerolinecolor="darkgrey",
linecolor="darkgrey",
linewidth=4,
titlefont=t,
tickfont=t)
q<-plot_ly(z=~Enrichment_Region, colors=color(10),
text=as.character(rownames(Enrichment_Region))) %>% add_surface() %>%
layout(scene = list(xaxis = x_axis, yaxis = y_axis, zaxis = z_axis))
q #must comment out for PDF generation via knitr (Pandoc).<div id="htmlwidget-abe0d5b12822ca5cb440" style="width:672px;height:480px;" class="plotly html-widget"></div>
<script type="application/json" data-for="htmlwidget-abe0d5b12822ca5cb440">{"x":{"visdat":{"2ee73db9e5dd":["function () ","plotlyVisDat"]},"cur_data":"2ee73db9e5dd","attrs":{"2ee73db9e5dd":{"z":{},"text":["Promoter","5'UTR","1stExon","Body","3'UTR"],"colors":["#BEBEBE","#CCB893","#DAB269","#E9AD3F","#F7A715","#FF9200","#FF6E00","#FF4900","#FF2400","#FF0000"],"alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"surface","inherit":true}},"layout":{"margin":{"b":40,"l":60,"t":25,"r":10},"scene":{"xaxis":{"title":"CpG Region","type":"category","zeroline":true,"showline":true,"zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":16,"color":"black"},"tickfont":{"family":"times","size":16,"color":"black"}},"yaxis":{"title":"Gene Region","type":"category","zeroline":true,"showline":true,"zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":16,"color":"black"},"tickfont":{"family":"times","size":16,"color":"black"}},"zaxis":{"title":"Number of DMPs","zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":16,"color":"black"},"tickfont":{"family":"times","size":16,"color":"black"}}},"hovermode":"closest","showlegend":false,"legend":{"yanchor":"top","y":0.5}},"source":"A","config":{"modeBarButtonsToAdd":["hoverclosest","hovercompare"],"showSendToCloud":false},"data":[{"colorbar":{"title":"Enrichment_Region","ticklen":2,"len":0.5,"lenmode":"fraction","y":1,"yanchor":"top"},"colorscale":[["0","rgba(190,190,190,1)"],["0.0416666666666666","rgba(196,188,174,1)"],["0.0833333333333333","rgba(201,185,158,1)"],["0.125","rgba(206,183,142,1)"],["0.166666666666667","rgba(212,181,126,1)"],["0.208333333333333","rgba(217,179,110,1)"],["0.25","rgba(222,177,95,1)"],["0.291666666666667","rgba(228,175,80,1)"],["0.333333333333333","rgba(233,173,63,1)"],["0.375","rgba(238,171,50,1)"],["0.416666666666667","rgba(244,169,35,1)"],["0.458333333333333","rgba(248,164,19,1)"],["0.5","rgba(251,157,11,1)"],["0.541666666666667","rgba(254,149,3,1)"],["0.583333333333333","rgba(255,137,0,1)"],["0.625","rgba(255,124,0,1)"],["0.666666666666667","rgba(255,110,0,1)"],["0.708333333333333","rgba(255,97,0,1)"],["0.75","rgba(255,83,0,1)"],["0.791666666666667","rgba(255,69,0,1)"],["0.833333333333333","rgba(255,57,0,1)"],["0.875","rgba(255,42,0,1)"],["0.916666666666667","rgba(255,30,0,1)"],["0.958333333333333","rgba(255,19,0,1)"],["1","rgba(255,0,0,1)"]],"showscale":true,"z":[[0.1164621465399,0.102998995174501,0.124221049754897,0.146041950369168,0.115637795393847,0.103793295570619],[0.0530358898721731,0.0622389306599833,0.0569429198682766,0.0741838816628411,0.0573958674975402,0.0576832151300236],[0.0588487972508591,0.0489130434782609,0.0623832648487112,0.0746423541620339,0.0625,0.037037037037037],[0.0523911393278587,0.0493794088757925,0.0510093237983163,0.0633284583420387,0.0507863308501833,0.0473962571196094],[0.0485609908224182,0.0415879017013233,0.0554833116601647,0.0638297872340425,0.056393076493579,0.0479302832244009]],"text":["Promoter","5'UTR","1stExon","Body","3'UTR"],"type":"surface","frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.2,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script>
Due to the prominent signature of CpG Island-associated promoter methylation in iPSCs exposed to serum for failing and non-failing patients, we examined all DMPs present within this region via heatmap.
library(ComplexHeatmap)
library(dplyr)
##Import Data Matrix
# betaHM<-read.csv("../1_Input/EPIC.betaValues.csv", row.names = 1)
## Filters to Apply to DMP
pvalue_threshold=0.001
METHYLATION=0
DMP_location="Island"
Gene_region="TSS"
Samples<-AnnoTargets$Sample_Name
##Filter Differential Methylation Data
DMP.p05<-Results %>% filter(pval<pvalue_threshold)
DMP.p05<-DMP.p05 %>% dplyr::select(Row.names,
Methylation.Diff,
pval,
qval,
Relation_to_Island,
UCSC_RefGene_Group,
chr,
pos,
matches(Samples)) %>%
filter(abs(Methylation.Diff)>METHYLATION)
DMP.p05.Region<-DMP.p05 %>%
# filter(grepl(DMP_location, Relation_to_Island)) %>%
filter(grepl(Gene_region, UCSC_RefGene_Group)) %>%
dplyr::select(matches(AnnoTargets$Sample_Name)) %>%
data.matrix()
#Import the Index File
LVAD_Counts_Data <- targets
rownames(LVAD_Counts_Data)<-targets$Sample_Name
Index<-LVAD_Counts_Data %>% dplyr::select(Sample_Group)
Index<-as.data.frame(Index)
paletteLength <- 100
ann_colors = list(Sample_Group = c(DCM="darkcyan", CON="darkgray"), Outcome = c(Bad = "firebrick2", Good = "darkgoldenrod2", CON = "black"))
myColor <- colorRampPalette(c("dodgerblue4", "white", "goldenrod2"))(paletteLength)
pheatmap::pheatmap(DMP.p05.Region, scale="row",
cluster_cols = TRUE,
cluster_rows = TRUE,
#breaks = myBreaks,
cutree_cols = 2,
cutree_rows = 2,
angle_col = 45,
fontsize_col = 8,
color = myColor,
show_rownames = FALSE,
border_color = NA,
annotation_col = Index,
annotation_colors=ann_colors,
filename = paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_", DMP_location, ".", Gene_region,".heatmap.pdf"))
pheatmap::pheatmap(DMP.p05.Region, scale="row",
cluster_cols = TRUE,
cluster_rows = TRUE,
#breaks = myBreaks,
cutree_cols = 2,
cutree_rows = 2,
angle_col = 45,
fontsize_col = 8,
color = myColor,
show_rownames = FALSE,
border_color = NA,
annotation_col = Index,
annotation_colors=ann_colors)# Load packages
library(dplyr)
library(ggplot2)
library(ggrepel)
library(openxlsx)
Results<-read.xlsx(paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_DMPs.xlsx"), sheet = "Unfiltered")
#Read data from the web
Volcano_data = mutate(Results, sig=ifelse(Results$pval<0.05 & abs(Results$Methylation.Diff)>5, "P<0.05 and |Methylation| > 5%", "Not Sig"), minuslogpvalue = -log(pval), Methylation=Methylation.Diff)
#Split gene names for labelling
Volcano_data_split<-Volcano_data %>% mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>% unnest(UCSC_RefGene_Name) %>% distinct()
max(Volcano_data$minuslogpvalue, na.rm = TRUE)## [1] 15.86107
# Results<-Results %>% filter(grepl("TSS", UCSC_RefGene_Group))
#plot the ggplot
p = ggplot(Volcano_data_split, aes(Methylation, minuslogpvalue)) + theme(panel.background = element_rect("white", colour = "black", size=2), panel.grid.major = element_line(colour = "gray50", size=.75), panel.grid.minor = element_line(colour = "gray50", size=0.4)) +
geom_point(aes(fill=sig, size = minuslogpvalue), colour="grey", shape=21, stroke = 0, alpha = 8/10) + labs(x=expression(Methylation_Change), y=expression(-Log[10](P-value))) + xlim(min(Volcano_data$Methylation, na.rm = TRUE),max(Volcano_data$Methylation, na.rm = TRUE))+ ylim(-0, max(Volcano_data$minuslogpvalue, na.rm = TRUE)) + geom_hline(yintercept = 0, size = 1) + geom_vline(xintercept=0, size=1)+
scale_fill_manual(values=c("grey", "darkgoldenrod2")) +
scale_size_continuous(range = c(.25, 4))
pdf(file = paste0("../2_Output/", COMPARISON, "/", COMPARISON, "Volcano.Plot.pdf"), height = 6, width = 10)
p+
geom_text_repel(data=top_n(filter(Volcano_data_split, pval<0.05, Methylation < 0, sig!="Not Sig"), 10, -Methylation), aes(label=UCSC_RefGene_Name)) +
geom_text_repel(data=top_n(filter(Volcano_data_split, pval<0.05, Methylation > 0, sig!="Not Sig"), 10, Methylation), aes(label=UCSC_RefGene_Name))
dev.off()## quartz_off_screen
## 2
library(openxlsx)
library(dplyr)
library(tidyr)
library(ComplexHeatmap)
library(minfi)
NUMBER = 20
STAT = 0.001
#Index
AnnoTargets<-read.metharray.sheet(base="../1_Input/IDAT", pattern=".csv")## [1] "../1_Input/IDAT/SampleSheet.csv"
rownames(AnnoTargets)<-AnnoTargets$Sample_Name
Index_combined<-AnnoTargets %>% dplyr::select(Sample_Group, Tissue, Sample_ID)
#iPSC Data
DMPs_iPSC<-read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
iPSC_stats<-DMPs_iPSC %>% dplyr::select(Methylation_iPSC = Methylation.Diff, pval_iPSC = pval, adj.P.Val_iPSC = qval, Name:Regulatory_Feature_Group)
#biopsies
DMPs_heart<-read.xlsx("../2_Output/heart_DCM_vs_CON/heart_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
heart_stats<-DMPs_heart %>% dplyr::select(Methylation_heart = Methylation.Diff, pval_heart = pval, adj.P.Val_heart = qval, Name:Regulatory_Feature_Group)
heart_index<-AnnoTargets %>% dplyr::filter(Tissue=="heart") %>% dplyr::select(Tissue, Sample_Group, Sample_ID)
#Beta
beta_all<-read.csv("../1_Input/beta_all.csv", row.names = 1)
#combine data
Combined_DMPs<-inner_join(iPSC_stats, heart_stats)
Combined_DMPs_Separated<-Combined_DMPs %>% mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>% unnest(UCSC_RefGene_Name) %>% distinct() %>% merge(., beta_all, by.x = "Name", by.y = 0)
# Select only co-methylated positions (iPSC and heart)
Combined_together<-Combined_DMPs_Separated %>% filter(Methylation_iPSC>0 & Methylation_heart>0 | Methylation_iPSC<0 & Methylation_heart<0) %>% arrange(desc(Methylation_iPSC)) %>% filter(pval_iPSC < STAT) %>% arrange(pval_iPSC)
#Find row number for top candidates
Candidates<-which(Combined_together$UCSC_RefGene_Name == "ATG7")
# Combined_together<-merge(Combined_together, beta_all, by.x = "Name", by.y = 0)
rownames(Combined_together)<-make.unique(Combined_together$UCSC_RefGene_Name, sep = ".")
#Create heatmap matrices and annotation
heart_hm<-Combined_together %>% dplyr::select(contains("NF") | contains("biopsy")) %>% data.matrix()
heart_index<-AnnoTargets %>% dplyr::filter(Tissue=="heart") %>% dplyr::select(Tissue, Sample_Group, Sample_ID)
iPSC_hm<-Combined_together %>% dplyr::select(contains("cells") & contains("co"),contains("cells") & contains("go"), contains("cells") & contains("bo")) %>% data.matrix()
iPSC_index<-AnnoTargets %>% dplyr::filter(Tissue=="iPSC") %>% dplyr::select(Tissue, Sample_Group, Sample_ID)
write.xlsx(Combined_together, "../2_Output/Overlapping.DMPs_iPSC.Biopsy.xlsx", overwrite = T)
# Venn Diagram
library(VennDiagram)
futile.logger::flog.threshold(futile.logger::ERROR, name = "VennDiagramLogger")## NULL
x<-list(iPSC = DMPs_iPSC$Name, heart = DMPs_heart$Name)
venn.diagram(x,fill = c("darkgray", "firebrick2"), alpha = c(0.75, 0.75), lty = 'blank', filename = "../2_Output/Overlapping_DMPs_iPSC.Biopsy.png", na = "remove")## [1] 1
# Heatmap
ann_colors = list(Sample_Group = c(DCM="#1b9e77", CON = "goldenrod2"), Tissue = c(heart = "coral2", iPSC = "darkgray"), Sample_ID = c(A = "white", B = "orange", C = "black", F = "red", G = "green", T = "blue", V = "purple"))
paletteLength <- 100
myColor <- colorRampPalette(c("dodgerblue4", "white", "gold2"))(paletteLength)
#iPSC
heatmap_iPSC<-ComplexHeatmap::pheatmap(iPSC_hm, scale="row",
cluster_cols = F,
cluster_rows = T,
# angle_col = 45,
fontsize_col = 8,
color = myColor,
annotation_names_col = FALSE,
show_rownames = F,
border_color = NA,
annotation_colors = ann_colors,
annotation_col = iPSC_index)
heatmap_iPSC
ha = rowAnnotation(foo = anno_mark(at = c(1:10), labels = Combined_together$UCSC_RefGene_Name[1:10]))
#heart
heatmap_heart<-ComplexHeatmap::pheatmap(heart_hm, scale = "row",
cluster_cols = F,
cluster_rows = T,
# angle_col = 45,
fontsize_col = 8,
color = myColor,
show_rownames = F,
border_color = NA,
annotation_names_col = FALSE,
right_annotation = ha,
annotation_colors = ann_colors,
annotation_col = heart_index)
heatmap_heart
heatmap_iPSC + heatmap_heart
pdf(file="../2_Output/complexheatmap_combined.pdf", height = 5, width = 7, onefile = F)
heatmap_iPSC + heatmap_heart
dev.off()## quartz_off_screen
## 2
#Import Pepin et al. 2019 Combined methylation-RNA-sequencing dataset
Pepin_DMPs<-read.xlsx("../1_Input/Validation/HF.Effect_NR_Pre.v.CON_Annotated_DiffMeth.xlsx")###### Working example (from BED file)
library(monaLisa)
library(GenomicRanges)
library(SummarizedExperiment)
library(openxlsx)
library(dplyr)
library(TFBSTools)
library(JASPAR2020)
library(BSgenome.Hsapiens.UCSC.hg19)
mcparams <- BiocParallel::MulticoreParam(10L) #parallelization (10-core)
DMPs_iPSC<-read.xlsx("../3_Results/Overlapping.DMPs_iPSC.Biopsy.xlsx", startRow = 2)
bed<-DMPs_iPSC %>% dplyr::select(chr, pos, Methylation_iPSC) %>% transmute(seqnames=chr, start=pos-20, end=pos+20, width = 41, strand = "*", deltaMeth=Methylation_iPSC)
bed_mr<-as(bed, "GRanges")
# define bins by differential methylation
bins <- bin(x = bed_mr$deltaMeth, binmode = "equalN", nElement = 100, minAbsX = 1)
table(bins)## bins
## [-6.06,-1.5] (-1.5,1.02] (1.02,7.75]
## 100 226 100
pdf(paste0("../2_Output/_bins.pdf"), width = 7.5, height = 5)
plotBinDensity(bed_mr$deltaMeth, bins, legend = "topright")
dev.off()## quartz_off_screen
## 2
# get PWMs from JASPAR
pwms <- getMatrixSet(JASPAR2020,
opts = list(matrixtype = "PWM",
tax_group = "vertebrates"))
# trim bed file for sequenes that are consistent
lmrsel <- trim(resize(bed_mr, width = median(width(bed_mr)), fix = "center"))
# get sequences from mouse genome
lmrseqs <- getSeq(BSgenome.Hsapiens.UCSC.hg19, bed_mr)
# GC proportion (bias)
plotBinDiagnostics(seqs = lmrseqs, bins = bins, aspect = "GCfrac")
plotBinDiagnostics(seqs = lmrseqs, bins = bins, aspect = "dinucfreq")
# run motif enrichment
se <- calcBinnedMotifEnrR(seqs = lmrseqs, bins = bins, pwmL = pwms, BPPARAM = BiocParallel::MulticoreParam(8))
# Filter results
Test<-as.data.frame(assays(se))
sel <- apply(assay(se, "negLog10P"), 1,
function(x) max(abs(x), 0, na.rm = TRUE)) > 1.0
sum(sel)## [1] 65
#> [1] 59
seSel <- se[sel, ]
# plot
pdf("../2_Output/Motifs.pdf", width = 11, height = 10)
plotMotifHeatmaps(x = seSel, which.plots = c("log2enr", "negLog10P"),
width = 2.0, cluster = TRUE, maxEnr = 2, maxSig = 10,
show_motif_GC = TRUE, show_dendrogram = T,show_seqlogo = TRUE)
dev.off()## quartz_off_screen
## 2
plotMotifHeatmaps(x = seSel, which.plots = c("log2enr", "negLog10P"),
width = 2.0, cluster = TRUE, maxEnr = 2, maxSig = 10,
show_motif_GC = TRUE, show_dendrogram = T,show_seqlogo = TRUE)All packages and setting are acquired using the following command:
options(kableExtra.latex.load_packages = FALSE)
Run_tE<-Sys.time()
Run_time<-Run_tE - Run_tS
Run_time## Time difference of 14.97141 mins
library(kableExtra)
sinfo<-devtools::session_info()
sinfo$platform## setting value
## version R version 4.1.2 (2021-11-01)
## os macOS Big Sur 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Berlin
## date 2021-12-31
## pandoc 2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)
sinfo$packages %>% kable(
align="c",
caption="Packages and Required Dependencies") %>%
kable_styling(latex_options=c("repeat_header", "condensed"))| package | ondiskversion | loadedversion | path | loadedpath | attached | is_base | date | source | md5ok | library | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| abind | abind | 1.4.5 | 1.4-5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/abind | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/abind | FALSE | FALSE | 2016-07-21 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| annotate | annotate | 1.72.0 | 1.72.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/annotate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/annotate | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| AnnotationDbi | AnnotationDbi | 1.56.2 | 1.56.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/AnnotationDbi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/AnnotationDbi | TRUE | FALSE | 2021-11-09 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| askpass | askpass | 1.1 | 1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/askpass | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/askpass | FALSE | FALSE | 2019-01-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| assertthat | assertthat | 0.2.1 | 0.2.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/assertthat | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/assertthat | FALSE | FALSE | 2019-03-21 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| backports | backports | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/backports | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/backports | FALSE | FALSE | 2021-11-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| base64 | base64 | 2.0 | 2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64 | FALSE | FALSE | 2016-05-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| base64enc | base64enc | 0.1.3 | 0.1-3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64enc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64enc | FALSE | FALSE | 2015-07-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| beanplot | beanplot | 1.2 | 1.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beanplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beanplot | FALSE | FALSE | 2014-09-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Biobase | Biobase | 2.54.0 | 2.54.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biobase | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biobase | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocFileCache | BiocFileCache | 2.2.0 | 2.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocFileCache | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocFileCache | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocGenerics | BiocGenerics | 0.40.0 | 0.40.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocGenerics | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocGenerics | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocIO | BiocIO | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocIO | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocIO | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocParallel | BiocParallel | 1.28.2 | 1.28.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocParallel | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocParallel | FALSE | FALSE | 2021-11-25 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| biomaRt | biomaRt | 2.50.1 | 2.50.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/biomaRt | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/biomaRt | TRUE | FALSE | 2021-11-21 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Biostrings | Biostrings | 2.62.0 | 2.62.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bit | bit | 4.0.4 | 4.0.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit | FALSE | FALSE | 2020-08-04 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bit64 | bit64 | 4.0.5 | 4.0.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit64 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit64 | FALSE | FALSE | 2020-08-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bitops | bitops | 1.0.7 | 1.0-7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bitops | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bitops | FALSE | FALSE | 2021-04-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| blob | blob | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/blob | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/blob | FALSE | FALSE | 2021-07-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| broom | broom | 0.7.10 | 0.7.10 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/broom | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/broom | FALSE | FALSE | 2021-10-31 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BSgenome | BSgenome | 1.62.0 | 1.62.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BSgenome | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BSgenome | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BSgenome.Hsapiens.UCSC.hg19 | BSgenome.Hsapiens.UCSC.hg19 | 1.4.3 | 1.4.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BSgenome.Hsapiens.UCSC.hg19 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BSgenome.Hsapiens.UCSC.hg19 | TRUE | FALSE | 2021-12-02 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bslib | bslib | 0.3.1 | 0.3.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bslib | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bslib | FALSE | FALSE | 2021-10-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bumphunter | bumphunter | 1.36.0 | 1.36.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bumphunter | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bumphunter | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cachem | cachem | 1.0.6 | 1.0.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cachem | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cachem | FALSE | FALSE | 2021-08-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| calibrate | calibrate | 1.7.7 | 1.7.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/calibrate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/calibrate | TRUE | FALSE | 2020-06-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| callr | callr | 3.7.0 | 3.7.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/callr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/callr | FALSE | FALSE | 2021-04-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| car | car | 3.0.12 | 3.0-12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/car | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/car | FALSE | FALSE | 2021-11-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| carData | carData | 3.0.4 | 3.0-4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/carData | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/carData | FALSE | FALSE | 2020-05-22 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| caTools | caTools | 1.18.2 | 1.18.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/caTools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/caTools | FALSE | FALSE | 2021-03-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cellranger | cellranger | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cellranger | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cellranger | FALSE | FALSE | 2016-07-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| checkmate | checkmate | 2.0.0 | 2.0.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/checkmate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/checkmate | FALSE | FALSE | 2020-02-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| circlize | circlize | 0.4.13 | 0.4.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/circlize | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/circlize | FALSE | FALSE | 2021-06-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cli | cli | 3.1.0 | 3.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cli | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cli | FALSE | FALSE | 2021-10-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| clue | clue | 0.3.60 | 0.3-60 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/clue | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/clue | FALSE | FALSE | 2021-10-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cluster | cluster | 2.1.2 | 2.1.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cluster | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cluster | FALSE | FALSE | 2021-04-17 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| CNEr | CNEr | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CNEr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CNEr | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| codetools | codetools | 0.2.18 | 0.2-18 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/codetools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/codetools | FALSE | FALSE | 2020-11-04 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| colorspace | colorspace | 2.0.2 | 2.0-2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/colorspace | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/colorspace | FALSE | FALSE | 2021-06-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ComplexHeatmap | ComplexHeatmap | 2.11.1 | 2.11.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ComplexHeatmap | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ComplexHeatmap | TRUE | FALSE | 2021-11-26 | Github (jokergoo/ComplexHeatmap@826b321) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| corrplot | corrplot | 0.92 | 0.92 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/corrplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/corrplot | TRUE | FALSE | 2021-11-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cowplot | cowplot | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cowplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cowplot | TRUE | FALSE | 2020-12-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| crayon | crayon | 1.4.2 | 1.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crayon | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crayon | FALSE | FALSE | 2021-10-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| crosstalk | crosstalk | 1.2.0 | 1.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crosstalk | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crosstalk | FALSE | FALSE | 2021-11-04 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| curl | curl | 4.3.2 | 4.3.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/curl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/curl | FALSE | FALSE | 2021-06-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| data.table | data.table | 1.14.2 | 1.14.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/data.table | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/data.table | TRUE | FALSE | 2021-09-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DBI | DBI | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DBI | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DBI | FALSE | FALSE | 2021-01-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| dbplyr | dbplyr | 2.1.1 | 2.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dbplyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dbplyr | FALSE | FALSE | 2021-04-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DelayedArray | DelayedArray | 0.20.0 | 0.20.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedArray | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedArray | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DelayedMatrixStats | DelayedMatrixStats | 1.16.0 | 1.16.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedMatrixStats | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedMatrixStats | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| desc | desc | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/desc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/desc | FALSE | FALSE | 2021-09-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DESeq2 | DESeq2 | 1.34.0 | 1.34.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DESeq2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DESeq2 | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| devtools | devtools | 2.4.3 | 2.4.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/devtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/devtools | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| digest | digest | 0.6.29 | 0.6.29 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest | FALSE | FALSE | 2021-12-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DirichletMultinomial | DirichletMultinomial | 1.36.0 | 1.36.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DirichletMultinomial | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DirichletMultinomial | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| doParallel | doParallel | 1.0.16 | 1.0.16 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doParallel | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doParallel | FALSE | FALSE | 2020-10-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| doRNG | doRNG | 1.8.2 | 1.8.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doRNG | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doRNG | FALSE | FALSE | 2020-01-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| dplyr | dplyr | 1.0.7 | 1.0.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dplyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dplyr | TRUE | FALSE | 2021-06-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ellipsis | ellipsis | 0.3.2 | 0.3.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ellipsis | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ellipsis | FALSE | FALSE | 2021-04-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| evaluate | evaluate | 0.14 | 0.14 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/evaluate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/evaluate | FALSE | FALSE | 2019-05-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| fansi | fansi | 0.5.0 | 0.5.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fansi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fansi | FALSE | FALSE | 2021-05-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| farver | farver | 2.1.0 | 2.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/farver | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/farver | FALSE | FALSE | 2021-02-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| fastmap | fastmap | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fastmap | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fastmap | FALSE | FALSE | 2021-01-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ff | ff | 4.0.5 | 4.0.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ff | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ff | FALSE | FALSE | 2021-10-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| filelock | filelock | 1.0.2 | 1.0.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/filelock | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/filelock | FALSE | FALSE | 2018-10-05 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| foreach | foreach | 1.5.1 | 1.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreach | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreach | TRUE | FALSE | 2020-10-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| foreign | foreign | 0.8.81 | 0.8-81 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreign | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreign | FALSE | FALSE | 2020-12-22 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| formatR | formatR | 1.11 | 1.11 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/formatR | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/formatR | FALSE | FALSE | 2021-06-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Formula | Formula | 1.2.4 | 1.2-4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Formula | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Formula | TRUE | FALSE | 2020-10-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| fs | fs | 1.5.1 | 1.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fs | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fs | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| futile.logger | futile.logger | 1.4.3 | 1.4.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.logger | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.logger | TRUE | FALSE | 2016-07-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| futile.options | futile.options | 1.0.1 | 1.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.options | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.options | FALSE | FALSE | 2018-04-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| genefilter | genefilter | 1.76.0 | 1.76.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/genefilter | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/genefilter | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| geneplotter | geneplotter | 1.72.0 | 1.72.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/geneplotter | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/geneplotter | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| generics | generics | 0.1.1 | 0.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/generics | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/generics | FALSE | FALSE | 2021-10-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomeInfoDb | GenomeInfoDb | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDb | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDb | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomeInfoDbData | GenomeInfoDbData | 1.2.7 | 1.2.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDbData | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDbData | FALSE | FALSE | 2021-11-17 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomicAlignments | GenomicAlignments | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicAlignments | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicAlignments | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomicFeatures | GenomicFeatures | 1.46.1 | 1.46.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicFeatures | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicFeatures | TRUE | FALSE | 2021-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomicRanges | GenomicRanges | 1.46.1 | 1.46.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicRanges | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicRanges | TRUE | FALSE | 2021-11-18 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GEOquery | GEOquery | 2.62.1 | 2.62.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GEOquery | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GEOquery | FALSE | FALSE | 2021-11-16 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GetoptLong | GetoptLong | 1.0.5 | 1.0.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GetoptLong | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GetoptLong | FALSE | FALSE | 2020-12-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggplot2 | ggplot2 | 3.3.5 | 3.3.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggplot2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggplot2 | TRUE | FALSE | 2021-06-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggpubr | ggpubr | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggpubr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggpubr | TRUE | FALSE | 2020-06-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggrepel | ggrepel | 0.9.1 | 0.9.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggrepel | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggrepel | TRUE | FALSE | 2021-01-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggsignif | ggsignif | 0.6.3 | 0.6.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggsignif | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggsignif | TRUE | FALSE | 2021-09-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| glmnet | glmnet | 4.1.3 | 4.1-3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/glmnet | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/glmnet | FALSE | FALSE | 2021-11-02 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GlobalOptions | GlobalOptions | 0.1.2 | 0.1.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GlobalOptions | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GlobalOptions | FALSE | FALSE | 2020-06-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| glue | glue | 1.5.1 | 1.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/glue | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/glue | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GO.db | GO.db | 3.14.0 | 3.14.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GO.db | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GO.db | FALSE | FALSE | 2021-12-06 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| gridExtra | gridExtra | 2.3 | 2.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gridExtra | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gridExtra | TRUE | FALSE | 2017-09-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| gtable | gtable | 0.3.0 | 0.3.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtable | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtable | FALSE | FALSE | 2019-03-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| gtools | gtools | 3.9.2 | 3.9.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtools | TRUE | FALSE | 2021-06-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Haplin | Haplin | 7.2.3 | 7.2.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Haplin | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Haplin | TRUE | FALSE | 2020-09-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| HDF5Array | HDF5Array | 1.22.1 | 1.22.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/HDF5Array | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/HDF5Array | FALSE | FALSE | 2021-11-14 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| highr | highr | 0.9 | 0.9 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/highr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/highr | FALSE | FALSE | 2021-04-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Hmisc | Hmisc | 4.6.0 | 4.6-0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Hmisc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Hmisc | TRUE | FALSE | 2021-10-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| hms | hms | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/hms | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/hms | FALSE | FALSE | 2021-09-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| htmlTable | htmlTable | 2.3.0 | 2.3.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlTable | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlTable | FALSE | FALSE | 2021-10-12 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| htmltools | htmltools | 0.5.2 | 0.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmltools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmltools | FALSE | FALSE | 2021-08-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| htmlwidgets | htmlwidgets | 1.5.4 | 1.5.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlwidgets | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlwidgets | FALSE | FALSE | 2021-09-08 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| httpuv | httpuv | 1.6.3 | 1.6.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httpuv | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httpuv | FALSE | FALSE | 2021-09-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| httr | httr | 1.4.2 | 1.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httr | FALSE | FALSE | 2020-07-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| IlluminaHumanMethylation450kanno.ilmn12.hg19 | IlluminaHumanMethylation450kanno.ilmn12.hg19 | 0.6.0 | 0.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kanno.ilmn12.hg19 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kanno.ilmn12.hg19 | TRUE | FALSE | 2021-11-17 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| IlluminaHumanMethylation450kmanifest | IlluminaHumanMethylation450kmanifest | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kmanifest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kmanifest | TRUE | FALSE | 2021-11-17 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| illuminaio | illuminaio | 0.36.0 | 0.36.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/illuminaio | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/illuminaio | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| IRanges | IRanges | 2.28.0 | 2.28.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| iterators | iterators | 1.0.13 | 1.0.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/iterators | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/iterators | TRUE | FALSE | 2020-10-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| JASPAR2020 | JASPAR2020 | 0.99.10 | 0.99.10 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/JASPAR2020 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/JASPAR2020 | TRUE | FALSE | 2021-12-06 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| jpeg | jpeg | 0.1.9 | 0.1-9 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jpeg | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jpeg | FALSE | FALSE | 2021-07-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| jquerylib | jquerylib | 0.1.4 | 0.1.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jquerylib | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jquerylib | FALSE | FALSE | 2021-04-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| jsonlite | jsonlite | 1.7.2 | 1.7.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jsonlite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jsonlite | FALSE | FALSE | 2020-12-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| kableExtra | kableExtra | 1.3.4 | 1.3.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/kableExtra | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/kableExtra | TRUE | FALSE | 2021-02-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| KEGGREST | KEGGREST | 1.34.0 | 1.34.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/KEGGREST | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/KEGGREST | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| knitr | knitr | 1.36 | 1.36 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/knitr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/knitr | TRUE | FALSE | 2021-09-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| labeling | labeling | 0.4.2 | 0.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/labeling | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/labeling | FALSE | FALSE | 2020-10-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lambda.r | lambda.r | 1.2.4 | 1.2.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lambda.r | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lambda.r | FALSE | FALSE | 2019-09-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| later | later | 1.3.0 | 1.3.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/later | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/later | FALSE | FALSE | 2021-08-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lattice | lattice | 0.20.45 | 0.20-45 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lattice | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lattice | TRUE | FALSE | 2021-09-22 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| latticeExtra | latticeExtra | 0.6.29 | 0.6-29 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/latticeExtra | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/latticeExtra | FALSE | FALSE | 2019-12-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lazyeval | lazyeval | 0.2.2 | 0.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lazyeval | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lazyeval | FALSE | FALSE | 2019-03-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lifecycle | lifecycle | 1.0.1 | 1.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lifecycle | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lifecycle | FALSE | FALSE | 2021-09-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| limma | limma | 3.50.0 | 3.50.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/limma | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/limma | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| locfit | locfit | 1.5.9.4 | 1.5-9.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/locfit | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/locfit | TRUE | FALSE | 2020-03-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| magick | magick | 2.7.3 | 2.7.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magick | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magick | FALSE | FALSE | 2021-08-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| magrittr | magrittr | 2.0.1 | 2.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magrittr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magrittr | TRUE | FALSE | 2020-11-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| MASS | MASS | 7.3.54 | 7.3-54 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS | TRUE | FALSE | 2021-05-03 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Matrix | Matrix | 1.3.4 | 1.3-4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix | FALSE | FALSE | 2021-06-01 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| MatrixGenerics | MatrixGenerics | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MatrixGenerics | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MatrixGenerics | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| matrixStats | matrixStats | 0.61.0 | 0.61.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/matrixStats | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/matrixStats | TRUE | FALSE | 2021-09-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| mclust | mclust | 5.4.8 | 5.4.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mclust | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mclust | FALSE | FALSE | 2021-11-05 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| memoise | memoise | 2.0.1 | 2.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/memoise | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/memoise | FALSE | FALSE | 2021-11-26 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| mgcv | mgcv | 1.8.38 | 1.8-38 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mgcv | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mgcv | FALSE | FALSE | 2021-10-06 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| mime | mime | 0.12 | 0.12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mime | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mime | FALSE | FALSE | 2021-09-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| minfi | minfi | 1.40.0 | 1.40.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/minfi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/minfi | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| monaLisa | monaLisa | 1.0.0 | 1.0.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/monaLisa | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/monaLisa | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| multtest | multtest | 2.50.0 | 2.50.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/multtest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/multtest | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| munsell | munsell | 0.5.0 | 0.5.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/munsell | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/munsell | FALSE | FALSE | 2018-06-12 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| nlme | nlme | 3.1.153 | 3.1-153 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nlme | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nlme | FALSE | FALSE | 2021-09-07 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| nnet | nnet | 7.3.16 | 7.3-16 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nnet | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nnet | FALSE | FALSE | 2021-05-03 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| nor1mix | nor1mix | 1.3.0 | 1.3-0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nor1mix | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nor1mix | FALSE | FALSE | 2019-06-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| openssl | openssl | 1.4.5 | 1.4.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl | FALSE | FALSE | 2021-09-02 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| openxlsx | openxlsx | 4.2.4 | 4.2.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openxlsx | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openxlsx | TRUE | FALSE | 2021-06-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pacman | pacman | 0.5.1 | 0.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pacman | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pacman | TRUE | FALSE | 2019-03-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pheatmap | pheatmap | 1.0.12 | 1.0.12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pheatmap | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pheatmap | TRUE | FALSE | 2019-01-04 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pillar | pillar | 1.6.4 | 1.6.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pillar | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pillar | FALSE | FALSE | 2021-10-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pkgbuild | pkgbuild | 1.2.1 | 1.2.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgbuild | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgbuild | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pkgconfig | pkgconfig | 2.0.3 | 2.0.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgconfig | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgconfig | FALSE | FALSE | 2019-09-22 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pkgload | pkgload | 1.2.4 | 1.2.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgload | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgload | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| plotly | plotly | 4.10.0 | 4.10.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plotly | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plotly | TRUE | FALSE | 2021-10-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| plyr | plyr | 1.8.6 | 1.8.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plyr | FALSE | FALSE | 2020-03-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| png | png | 0.1.7 | 0.1-7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/png | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/png | FALSE | FALSE | 2013-12-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| poweRlaw | poweRlaw | 0.70.6 | 0.70.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/poweRlaw | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/poweRlaw | FALSE | FALSE | 2020-04-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pracma | pracma | 2.3.3 | 2.3.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pracma | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pracma | FALSE | FALSE | 2021-01-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| preprocessCore | preprocessCore | 1.56.0 | 1.56.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| prettyunits | prettyunits | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/prettyunits | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/prettyunits | FALSE | FALSE | 2020-01-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| processx | processx | 3.5.2 | 3.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/processx | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/processx | FALSE | FALSE | 2021-04-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| progress | progress | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/progress | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/progress | FALSE | FALSE | 2019-05-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| promises | promises | 1.2.0.1 | 1.2.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/promises | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/promises | FALSE | FALSE | 2021-02-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ps | ps | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ps | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ps | FALSE | FALSE | 2021-02-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| purrr | purrr | 0.3.4 | 0.3.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/purrr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/purrr | FALSE | FALSE | 2020-04-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| quadprog | quadprog | 1.5.8 | 1.5-8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/quadprog | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/quadprog | FALSE | FALSE | 2019-11-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R.methodsS3 | R.methodsS3 | 1.8.1 | 1.8.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.methodsS3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.methodsS3 | FALSE | FALSE | 2020-08-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R.oo | R.oo | 1.24.0 | 1.24.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.oo | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.oo | FALSE | FALSE | 2020-08-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R.utils | R.utils | 2.11.0 | 2.11.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.utils | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.utils | FALSE | FALSE | 2021-09-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R6 | R6 | 2.5.1 | 2.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R6 | FALSE | FALSE | 2021-08-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rappdirs | rappdirs | 0.3.3 | 0.3.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rappdirs | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rappdirs | FALSE | FALSE | 2021-01-31 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| RColorBrewer | RColorBrewer | 1.1.2 | 1.1-2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RColorBrewer | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RColorBrewer | TRUE | FALSE | 2014-12-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Rcpp | Rcpp | 1.0.7 | 1.0.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp | FALSE | FALSE | 2021-07-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| RCurl | RCurl | 1.98.1.5 | 1.98-1.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RCurl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RCurl | FALSE | FALSE | 2021-09-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| readr | readr | 2.1.1 | 2.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readr | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| readxl | readxl | 1.3.1 | 1.3.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readxl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readxl | TRUE | FALSE | 2019-03-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| remotes | remotes | 2.4.2 | 2.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/remotes | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/remotes | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| reshape | reshape | 0.8.8 | 0.8.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape | FALSE | FALSE | 2018-10-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| reshape2 | reshape2 | 1.4.4 | 1.4.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape2 | TRUE | FALSE | 2020-04-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| restfulr | restfulr | 0.0.13 | 0.0.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/restfulr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/restfulr | FALSE | FALSE | 2017-08-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rhdf5 | rhdf5 | 2.38.0 | 2.38.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5 | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rhdf5filters | rhdf5filters | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5filters | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5filters | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Rhdf5lib | Rhdf5lib | 1.16.0 | 1.16.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rjson | rjson | 0.2.20 | 0.2.20 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rjson | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rjson | FALSE | FALSE | 2018-06-08 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rlang | rlang | 0.4.12 | 0.4.12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rlang | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rlang | FALSE | FALSE | 2021-10-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rmarkdown | rmarkdown | 2.11 | 2.11 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown | FALSE | FALSE | 2021-09-14 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rngtools | rngtools | 1.5.2 | 1.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rngtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rngtools | FALSE | FALSE | 2021-09-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rpart | rpart | 4.1.15 | 4.1-15 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rpart | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rpart | FALSE | FALSE | 2019-04-12 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rprojroot | rprojroot | 2.0.2 | 2.0.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rprojroot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rprojroot | FALSE | FALSE | 2020-11-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Rsamtools | Rsamtools | 2.10.0 | 2.10.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rsamtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rsamtools | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| RSQLite | RSQLite | 2.2.8 | 2.2.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RSQLite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RSQLite | FALSE | FALSE | 2021-08-21 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rstatix | rstatix | 0.7.0 | 0.7.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstatix | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstatix | FALSE | FALSE | 2021-02-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rstudioapi | rstudioapi | 0.13 | 0.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstudioapi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstudioapi | FALSE | FALSE | 2020-11-12 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rtracklayer | rtracklayer | 1.54.0 | 1.54.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rtracklayer | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rtracklayer | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rvest | rvest | 1.0.2 | 1.0.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rvest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rvest | FALSE | FALSE | 2021-10-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| S4Vectors | S4Vectors | 0.32.3 | 0.32.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors | TRUE | FALSE | 2021-11-21 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| sass | sass | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sass | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sass | FALSE | FALSE | 2021-05-12 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| scales | scales | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scales | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scales | FALSE | FALSE | 2020-05-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| scrime | scrime | 1.3.5 | 1.3.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scrime | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scrime | FALSE | FALSE | 2018-12-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| seqLogo | seqLogo | 1.60.0 | 1.60.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqLogo | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqLogo | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| sessioninfo | sessioninfo | 1.2.1 | 1.2.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sessioninfo | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sessioninfo | FALSE | FALSE | 2021-11-02 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| shape | shape | 1.4.6 | 1.4.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shape | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shape | FALSE | FALSE | 2021-05-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| shiny | shiny | 1.7.1 | 1.7.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shiny | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shiny | TRUE | FALSE | 2021-10-02 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| shinyMethyl | shinyMethyl | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shinyMethyl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shinyMethyl | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| siggenes | siggenes | 1.68.0 | 1.68.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/siggenes | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/siggenes | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| sm | sm | 2.2.5.7 | 2.2-5.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sm | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sm | FALSE | FALSE | 2021-09-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| sparseMatrixStats | sparseMatrixStats | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sparseMatrixStats | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sparseMatrixStats | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| stabs | stabs | 0.6.4 | 0.6-4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stabs | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stabs | FALSE | FALSE | 2021-01-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| stringi | stringi | 1.7.6 | 1.7.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringi | FALSE | FALSE | 2021-11-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| stringr | stringr | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringr | TRUE | FALSE | 2019-02-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| SummarizedExperiment | SummarizedExperiment | 1.24.0 | 1.24.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/SummarizedExperiment | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/SummarizedExperiment | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| survival | survival | 3.2.13 | 3.2-13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/survival | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/survival | TRUE | FALSE | 2021-08-24 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| svglite | svglite | 2.0.0 | 2.0.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/svglite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/svglite | FALSE | FALSE | 2021-02-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| systemfonts | systemfonts | 1.0.3 | 1.0.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/systemfonts | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/systemfonts | FALSE | FALSE | 2021-10-13 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| testthat | testthat | 3.1.1 | 3.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat | FALSE | FALSE | 2021-12-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| TFBSTools | TFBSTools | 1.32.0 | 1.32.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/TFBSTools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/TFBSTools | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| TFMPvalue | TFMPvalue | 0.0.8 | 0.0.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/TFMPvalue | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/TFMPvalue | FALSE | FALSE | 2018-05-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tibble | tibble | 3.1.6 | 3.1.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tibble | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tibble | FALSE | FALSE | 2021-11-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tidyr | tidyr | 1.1.4 | 1.1.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyr | TRUE | FALSE | 2021-09-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tidyselect | tidyselect | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyselect | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyselect | FALSE | FALSE | 2021-04-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tzdb | tzdb | 0.2.0 | 0.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tzdb | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tzdb | FALSE | FALSE | 2021-10-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| usethis | usethis | 2.1.3 | 2.1.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/usethis | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/usethis | FALSE | FALSE | 2021-10-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| utf8 | utf8 | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/utf8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/utf8 | FALSE | FALSE | 2021-07-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| vctrs | vctrs | 0.3.8 | 0.3.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/vctrs | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/vctrs | FALSE | FALSE | 2021-04-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| VennDiagram | VennDiagram | 1.7.1 | 1.7.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/VennDiagram | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/VennDiagram | TRUE | FALSE | 2021-12-02 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| vioplot | vioplot | 0.3.7 | 0.3.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/vioplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/vioplot | FALSE | FALSE | 2021-07-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| viridisLite | viridisLite | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/viridisLite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/viridisLite | FALSE | FALSE | 2021-04-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| webshot | webshot | 0.5.2 | 0.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/webshot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/webshot | FALSE | FALSE | 2019-11-22 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| wesanderson | wesanderson | 0.3.6 | 0.3.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/wesanderson | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/wesanderson | TRUE | FALSE | 2018-04-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| withr | withr | 2.4.3 | 2.4.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/withr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/withr | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| xfun | xfun | 0.28 | 0.28 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xfun | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xfun | FALSE | FALSE | 2021-11-04 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| XML | XML | 3.99.0.8 | 3.99-0.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XML | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XML | FALSE | FALSE | 2021-09-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| xml2 | xml2 | 1.3.3 | 1.3.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xml2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xml2 | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| xtable | xtable | 1.8.4 | 1.8-4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xtable | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xtable | FALSE | FALSE | 2019-04-21 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| XVector | XVector | 0.34.0 | 0.34.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| yaml | yaml | 2.2.1 | 2.2.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/yaml | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/yaml | FALSE | FALSE | 2020-02-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| zip | zip | 2.2.0 | 2.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zip | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zip | FALSE | FALSE | 2021-05-31 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| zlibbioc | zlibbioc | 1.40.0 | 1.40.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| zoo | zoo | 1.8.9 | 1.8-9 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zoo | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zoo | FALSE | FALSE | 2021-03-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library |