M2BIMS_Enrich_Analysis_Rshiny

Goal

The goal of this application is to facilitates functional enrichment analysis from differential expression results, and allow for quick and interactive visualization.

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Installation from GitHub

In a terminal :

git clone [email protected]:CamilleGodi/M2BIMS_Enrich_Analysis_Rshiny.git

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Dependancies

• BiocManager

• clusterProfiler

• DT

• shiny

• shinydashboard

• shinyalert

• plotly

• ReactomePA

• tidyverse

If not already existing on the computer, the program will try to install those libraries itself.

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Annotation libraries

Pre-installed annotation libraries from Bioconductor :

• org.At.tair.db (Arabidopsis thaliana)

• org.EcK12.eg.db (Escherichia coli (K12))

• org.Hs.eg.db (Homo sapiens)

• org.Mm.eg.db" (Mus musculus)

• org.Sc.sgd.db (Saccharomyces cerevisiae)

How to add a new organism

In ui.R :

• Add organism name in the list in line 36

In global.R :

• Add the corresponding organism annotation library from Bioconductor in load_libs_biocmanager

• Add the corresponding line to the conversion table : organism_conversion_table <- add_organism_in_conversion_table(organism_conversion_table, "Organism name", "org.Xx.xxx.db", "kegg_code", "reactome_name"), with kegg_code the 3- or 4-letters KEGG organism code ( see here ), org.Xx.xxx.db the organism annotation library name, and reactome_name the name of the organism in the ReactomePA package (NA if not available. Available : 'celegans', 'fly', 'human', 'mouse', 'rat', 'yeast' and 'zebrafish').

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Tutorial

1/ Select a CSV (or CSV2) file. It must have the following columns and none others : 'GeneName', 'ID', 'baseMean', 'log2FC', 'pval', 'padj'.

2/ Select the scientific name of the organism from which the data originates. Tip : you can type to search in the box.

3/ (Optional) Explore your data through the 'Whole data inspection' tab.

4/ Perform desired analysis (ORA or GSEA) through the appropriate tab.

Note : any plot can be downloaded by doing right-click > 'save image as'.

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Authors

• Victor BAILLEUL ( [email protected] )

• Camille GODI ( [email protected] )

• Benjamin MARSAC ( [email protected] )

• Komlan Dieu-Donné TOTO ( [email protected] )

This app is the result of a group work in second year of Bioinformatics Master's Degree, 'BIMS', year 2023-2024s, Université de Rouen Normandie ( URN ).

Acknowledgments :

We thank Solène Pety and Hélène Dauchel for their guidance and advices.