DESCRIPTION

Package: BUSpaRse
Type: Package
Title: kallisto | bustools R utilities
Version: 1.18.1
Date: 2024-07-31
Authors@R: 
    c(person("Lambda", "Moses", email = "dlu2@caltech.edu", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-7092-9427")),
    person("Lior", "Pachter", email = "lpachter@caltech.edu",
    role = c("aut", "ths"),
    comment = c(ORCID = "0000-0002-9164-6231")))
Description: 
    The kallisto | bustools pipeline is a fast and modular set of tools to
    convert single cell RNA-seq reads in fastq files into gene count or 
    transcript compatibility counts (TCC) matrices for downstream analysis.
    Central to this pipeline is the barcode, UMI, and set (BUS) file format.
    This package serves the following purposes: First, this package allows users
    to manipulate BUS format files as data frames in R and then convert them 
    into gene count or TCC matrices. Furthermore, since R and Rcpp code is 
    easier to handle than pure C++ code, users are encouraged to tweak the 
    source code of this package to experiment with new uses of BUS format and
    different ways to convert the BUS file into gene count matrix. Second, this 
    package can conveniently generate files required to generate gene count 
    matrices for spliced and unspliced transcripts for RNA velocity. Here 
    biotypes can be filtered and scaffolds and haplotypes can be removed, and
    the filtered transcriptome can be extracted and written to disk. Third, 
    this package implements utility functions to get transcripts and associated 
    genes required to convert BUS files to gene count matrices, to write the
    transcript to gene information in the format required by bustools, and to
    read output of bustools into R as sparses matrices.
BugReports: https://github.com/BUStools/BUSpaRse/issues
URL: https://github.com/BUStools/BUSpaRse
Imports: 
    AnnotationDbi,
    AnnotationFilter,
    biomaRt,
    BiocGenerics,
    Biostrings,
    BSgenome,
    dplyr,
    ensembldb,
    GenomeInfoDb,
    GenomicFeatures,
    GenomicRanges,
    ggplot2,
    IRanges,
    magrittr,
    Matrix,
    methods,
    plyranges,
    Rcpp,
    S4Vectors,
    stats,
    stringr,
    tibble,
    tidyr,
    utils,
    zeallot
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH
RoxygenNote: 7.1.1
Roxygen: list(markdown = TRUE)
Suggests: 
    knitr,
    rmarkdown,
    testthat,
    BiocStyle,
    txdbmaker,
    TENxBUSData,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    txdbmaker,
    BSgenome.Hsapiens.UCSC.hg38,
    EnsDb.Hsapiens.v86
VignetteBuilder: knitr
LazyData: TRUE
Collate: 
    'RcppExports.R'
    'annots_from_fa.R'
    'biotypes.R'
    'get_tx.R'
    'knee_plot.R'
    'sparse_matrix.R'
    'tr2g.R'
    'utils.R'
    'velocity.R'
    'velocity_methods.R'
Encoding: UTF-8
License: BSD_2_clause + file LICENSE
biocViews:
    SingleCell,
    RNASeq,
    WorkflowStep
SystemRequirements: GNU make
Depends: 
    R (>= 3.6)