README.md

In Elizaddh/pathview: What the Package Does (One Line, Title Case)

Pathview is a tool that maps, integrates and renders a wide variety of biological data on relevant pathway graphs. This github provides a R package for the automated analysis of RNAseq data starting from differential expression analysis, pathway analysis and pathway visualization. For those wanting to analyse RNAseq starting from reads, a workflow and a pipeline that runs in R is also provided to process raw/processed RNAseq reads and align and generate counts through qsar package using tools like rhistat2 (and other alignemnt tool, "yet to decide" ). Differential analysis tools like DESEQ2, edgeR and baySeq have been incorporated in the package. Users can chose to perform pathway analysis directly on gene data and visualize the data or run differential gene analysis before running pathway analysis. Publication ready figures like KEGG pathways and heatmap and table of expression of significant genes can be generated using the package.

Elizaddh/pathview documentation built on July 14, 2022, 6:39 p.m.