rgsepd: Gene Set Enrichment / Projection Displays

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R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

Author
Karl Stamm
Date of publication
None
Maintainer
Karl Stamm <karl.stamm@gmail.com>
License
GPL-3
Version
1.6.0

View on Bioconductor

Man pages

DisplayName
DisplayName
GSEPD_ChangeConditions
GSEPD_ChangeConditions
GSEPD_ChangeOutput
GSEPD_ChangeOutput
GSEPD_DEGHeatmap
Differentially Expressed Genes Heatmap
GSEPD_Export_DESeq
Export DESeqDataSet object
GSEPD_Heatmap
GSEPD_Heatmap
GSEPD_INIT
Initialization
GSEPD_PCA_Plot
Principle Components Analysis figure generation
GSEPD_PCA_Spec
Specialized PCA Plot
GSEPD_Process
Processing
GSEPD_ProcessAll
GSEPD_ProcessAll
GSEPD_PullDEG
Pull Differentially Expressed Genes
IlluminaBodymap
Sample RNA-Seq Counts data
IlluminaBodymapMeta
Metadata table for the included sample data
Name_to_RefSeq
Name to RefSeq
rgsepd-package
R/Gene Set Enrichment and Projection Displays

Files in this package

rgsepd/DESCRIPTION
rgsepd/NAMESPACE
rgsepd/NEWS
rgsepd/R
rgsepd/R/GOCAT_Engine.R
rgsepd/R/GSEPD_API.R
rgsepd/R/GSEPD_DEGHeatmap.R
rgsepd/R/GSEPD_Heatmap.R
rgsepd/R/GSEPD_INIT.R
rgsepd/R/GSEPD_PCA_Plot.R
rgsepd/R/GSEPD_Pairs_Plot.R
rgsepd/R/GSEPD_Process.R
rgsepd/R/GroupSignificance.R
rgsepd/R/lib.R
rgsepd/R/namechange.R
rgsepd/R/reversemapping.R
rgsepd/build
rgsepd/build/vignette.rds
rgsepd/data
rgsepd/data/IlluminaBodymap.csv.gz
rgsepd/data/IlluminaBodymapMeta.csv.gz
rgsepd/inst
rgsepd/inst/doc
rgsepd/inst/doc/rgsepd.R
rgsepd/inst/doc/rgsepd.Rnw
rgsepd/inst/doc/rgsepd.pdf
rgsepd/man
rgsepd/man/DisplayName.Rd
rgsepd/man/GSEPD_ChangeConditions.Rd
rgsepd/man/GSEPD_ChangeOutput.Rd
rgsepd/man/GSEPD_DEGHeatmap.Rd
rgsepd/man/GSEPD_Export_DESeq.Rd
rgsepd/man/GSEPD_Heatmap.Rd
rgsepd/man/GSEPD_INIT.Rd
rgsepd/man/GSEPD_PCA_Plot.Rd
rgsepd/man/GSEPD_PCA_Spec.Rd
rgsepd/man/GSEPD_Process.Rd
rgsepd/man/GSEPD_ProcessAll.Rd
rgsepd/man/GSEPD_PullDEG.Rd
rgsepd/man/IlluminaBodymap.Rd
rgsepd/man/IlluminaBodymapMeta.Rd
rgsepd/man/Name_to_RefSeq.Rd
rgsepd/man/rgsepd-package.Rd
rgsepd/vignettes
rgsepd/vignettes/rgsepd.Rnw