This R package contains several functions that compress major RNA-seq and ChIP-seq analysis steps into one-liners (okay, maybe two, I’m not perfect).
Objective
This package serves as a complement to an in-preparation manuscript and as a record of how the data was analyzed in addition to serving as a basis for the Payton Lab bulk RNA-seq and ChIP-seq analyses moving forwards.
What It Can Do
Ultimately, this package tries to make generic RNA-seq and ChIP-seq analyses as high-level and straightforward as possible. It does so by requiring only the path to a samplesheet containing sample metadata and file locations and the metadata variable of interest. It will then perform RNA or ChIP-seq analyses with DESeq2 or DiffBind, respectively, for all possible comparisons for the variable of interest and save the results for each analysis to disk.
You can feed it multiple p-value/FDR/fold change thresholds, and it will generate fairly nice plots for differentially expressed genes or differentially bound regions including PCA/MA plots, heatmaps, volcano plots, GO/pathway enrichment analyses, boxplots, etc., saving all of them as PDFs.
Usage
Please see the docs for a full reference and vignettes with examples (including steps like gene count quantification, peak calling, etc). 90% of the functionality can be viewed with ?RunDESeq2 and ?RunDiffBind after installation. The salmon, DESeq2, and DiffBind manuals and vignettes may also be helpful for understanding what’s going on under the hood and interpreting the output.
Issues
Please direct all complaints to management.
