sRAP: Simplified RNA-Seq Analysis Pipeline

This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

AuthorCharles Warden
Date of publicationNone
MaintainerCharles Warden <cwarden45@gmail.com>
LicenseGPL-3
Version1.14.0

View on Bioconductor

Files in this package

sRAP/CHANGES
sRAP/DESCRIPTION
sRAP/NAMESPACE
sRAP/R
sRAP/R/RNA.bdfunc.R sRAP/R/RNA.deg.R sRAP/R/RNA.norm.R sRAP/R/RNA.prepare.input.R sRAP/R/RNA.qc.R
sRAP/build
sRAP/build/vignette.rds
sRAP/data
sRAP/data/bdfunc.enrichment.human.rda
sRAP/data/bdfunc.enrichment.mouse.rda
sRAP/data/datalist
sRAP/inst
sRAP/inst/CITATION
sRAP/inst/Perl
sRAP/inst/Perl/tabulate_RPKM.pl
sRAP/inst/doc
sRAP/inst/doc/sRAP.R
sRAP/inst/doc/sRAP.Rnw
sRAP/inst/doc/sRAP.pdf
sRAP/inst/extdata
sRAP/inst/extdata/MiSeq_Sample_Description.txt
sRAP/inst/extdata/MiSeq_cufflinks_genes_truncate.txt
sRAP/inst/extdata/cufflinks
sRAP/inst/extdata/cufflinks/SRR493372_truncated.fpkm_tracking
sRAP/inst/extdata/cufflinks/SRR493373_truncated.fpkm_tracking
sRAP/inst/extdata/cufflinks/SRR493374_truncated.fpkm_tracking
sRAP/inst/extdata/cufflinks/SRR493375_truncated.fpkm_tracking
sRAP/inst/extdata/cufflinks/SRR493376_truncated.fpkm_tracking
sRAP/inst/extdata/cufflinks/SRR493377_truncated.fpkm_tracking
sRAP/man
sRAP/man/RNA.bdfunc.fc.Rd sRAP/man/RNA.bdfunc.signal.Rd sRAP/man/RNA.deg.Rd sRAP/man/RNA.norm.Rd sRAP/man/RNA.prepare.input.Rd sRAP/man/RNA.qc.Rd sRAP/man/bdfunc.enrichment.human.Rd sRAP/man/bdfunc.enrichment.mouse.Rd
sRAP/vignettes
sRAP/vignettes/GLI1_UP_V1_fc.pdf
sRAP/vignettes/GLI1_UP_V1_signal.pdf
sRAP/vignettes/MiSeq_TGFB1_box_plot.pdf
sRAP/vignettes/MiSeq_box_plot.pdf
sRAP/vignettes/MiSeq_cluster.pdf
sRAP/vignettes/MiSeq_heatmap.pdf
sRAP/vignettes/MiSeq_hist.pdf
sRAP/vignettes/MiSeq_pca.pdf
sRAP/vignettes/Thumbs.db
sRAP/vignettes/sRAP.Rnw
sRAP/vignettes/sRAP.bbl
sRAP/vignettes/sRAP.bib
sRAP/vignettes/sRAP_Workflow.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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