Reference

RNA-seq analysis

Functions that perform DESeq2 analyses, utilizing the utility and plotting functions to generate output tables and figures. These are the crux of the RNA-seq portion of the package and what most users should use.

RunDESeq2()

Run DESeq2 analyses

ProcessDEGs()

Extract, visualize, and save DEG lists

RNA-seq Plotting

Functions that generate plots for RNA-seq data. Calling these individually can sometimes be useful.

PlotRNABoxplots()

Plot gene counts as box plots

PlotRNACombinedHeatmaps()

Generate gene heatmaps for all DEGs from a list of DESeq2 results

PlotRNADEGPCAs()

Plot PCAs from variance stabilized counts for differentially expressed genes

PlotRNAEDAPCAs()

Plot PCAs from variance stabilized counts for EDA

PlotRNAHeatmaps()

Generate per comparison DEG heatmaps for a list of DESeq2 results

PlotRNASampleDistances()

Visualize sample distances from variance stabilized counts

PlotRNAVarianceTransformations()

Perform and visualize different variance stabilization transformations

PlotRNAVolcanoes()

Create volcano plots from a list of DESeq2 Results objects

ChIP-seq analysis

Functions that perform ChIPQC/DiffBind analyses, utilizing the utility and plotting functions to generate output tables and figures. These are the crux of the ChIP-seq portion of the package and what most users should use.

RunChIPQC()

Run ChIPQC on a sample sheet

RunDiffBind()

Run DiffBind analysis on a samplesheet

ProcessDBRs()

Extract, visualize, and save DBRs

ChIP-seq Plotting

Functions that generate plots for ChIP-seq data. Calling these individually can sometimes be useful.

PlotChIPAnnos()

Plot ChIP annotation breakdowns

PlotChIPHeatmaps()

Plot ChIP heatmaps

PlotChIPPCAs()

Plot ChIP PCAs

Enrichment Analyses

This function performs GO/pathway enrichment analysis for lists of genes resulting from both RNA and ChIP-seq analyses.

PlotEnrichments()

Perform GO/Pathway enrichment for DEGs or DBRs via enrichR

Internal utilities

Functions used to create directory structure and save output. Users shouldn’t need to call these explicitely.

CreateOutputStructure()

Create output directory structure

SaveResults()

Save results