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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sRAP")
AuthorCharles Warden
Bioconductor views DifferentialExpression GO GeneExpression GeneSetEnrichment Microarray Preprocessing QualityControl RNAseq Statistics Visualization
Date of publicationNone
MaintainerCharles Warden <cwarden45@gmail.com>
LicenseGPL-3
Version1.16.0

View on Bioconductor

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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