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rgsepd (version 1.2.0)

Gene Set Enrichment / Projection Displays

Description

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.

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Version

Version

1.2.0

License

GPL-3

Maintainer

Karl Stamm

Last Published

February 15th, 2017

Functions in rgsepd (1.2.0)

GSEPD_PCA_Plot

Principle Components Analysis figure generation
GSEPD_Process

Processing
GSEPD_ChangeConditions

GSEPD_ChangeConditions
DisplayName

DisplayName
GSEPD_PCA_Spec

Specialized PCA Plot
GSEPD_INIT

Initialization
GSEPD_DEGHeatmap

Differentially Expressed Genes Heatmap
GSEPD_Export_DESeq

Export DESeqDataSet object
GSEPD_ChangeOutput

GSEPD_ChangeOutput
GSEPD_Heatmap

GSEPD_Heatmap
GSEPD_PullDEG

Pull Differentially Expressed Genes
IlluminaBodymap

Sample RNA-Seq Counts data
GSEPD_ProcessAll

GSEPD_ProcessAll
IlluminaBodymapMeta

Metadata table for the included sample data
Name_to_RefSeq

Name to RefSeq
rgsepd-package

R/Gene Set Enrichment and Projection Displays