jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Provides a function toolkit to facilite reproducible RNA-Seq DGE analysis and improve TBio "branding" by standardizing several types of commmon plots. The functions can be grouped into three categories (DGE workflow, DGE plotting tools and mapping/unit conversion functions. The DGE workflow functions include: Function initDgeObj which builds a DGEobj data structure from counts and annotation; Function runEdgeRNorm which normalizes counts; Function runVoom runs limma voom and lmfit adding additional data to the DGEobj; Function runSVA for detrending unknown covariates. A variety of QC plots are produced to evaluate data quality. The DGE Plotting tools are suitable for downstream analysis visualizations and include: profilePlot, volcanoPlot, comparePlot, plotPvalHist, ggplotMDS and others. Function convertCounts is supplied to convert a counts matrix and produce CPM/TPM/FPKM, logged or not, normalized or not.

install.packages("remotes")
remotes::install_github("jrthompson54/DGE.Tools2")