timecourseRnaseq

The timecourseRnaseq package currently has one primary function:

check_enrichment()

which performs overrepresentation analyses (using hypergeometric test) and returns the enrichment results as a table. Additionally, the function also plots the enrichment results by default.

Citation

Das, B. (2022). timecourseRnaseq: an R package to analyze time-course RNAseq data. DOI: 10.5281/zenodo.7069315

for other formats, find it on google scholar

Installation

You can install the development version from GitHub with:

install.packages("devtools")
devtools::install_github("biplabendu/timecourseRnaseq")

Usage

?check_enrichment

library(timecourseRnaseq)
some.beau.genes <- c("BBA_00100", "BBA_01000", "BBA_10000", "BBA_10001", "BBA_10002", "BBA_10003", "BBA_10004")

## GO enrichments + plot
check_enrichment(some.beau.genes, org="beau")

## pfam enrichments (no plot)
check_enrichment(some.beau.genes, org="beau", what="pfams", plot=F)

## pfam enrichments + plot + long-formatted enrichment results
check_enrichment(some.beau.genes, org="beau", what="pfams", plot=T, expand=T)
   # please note, expand=T works only if the annotation file contains a column 
   # named "gene_desc" that contains descriptions of genes

## specify your own annotation file (?check_enrichment)
some.speciesXX.genes <- c("genes", "of", "interest", "from", "speciesXX") # geneset
path <- "path/to/speciesXX/annotation/file.csv" 
check_enrichment(geneset=some.speciesXX.genes, path_to_annot = path, what="GOs") # double-check if sep needs to be specified

The annotation files for the four organisms (cflo_annots, beau_annots, ophio_cflo_annots, ophio_kim_annots) are provided.
To see an annotation file, just type the following:

## org = "beau"
head(beau_annots)

## org = "cflo"
head(cflo_annots)