Package: SeqGSEA 1.53.0

Xi Wang

SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.

Authors:Xi Wang <[email protected]>

SeqGSEA_1.53.0.tar.gz
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SeqGSEA_1.53.0.tgz(r-4.6-any)SeqGSEA_1.53.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SeqGSEA/json (API)

# Install 'SeqGSEA' in R:

install.packages('SeqGSEA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

DEscore - Pre-calculated DE/DS scores
DEscore.perm - Pre-calculated DE/DS scores
DSscore - Pre-calculated DE/DS scores
DSscore.perm - Pre-calculated DE/DS scores
GS_example - SeqGeneSet object example
RCS_example - ReadCountSet object example

On BioConductor:SeqGSEA-1.53.0(bioc 3.24)SeqGSEA-1.52.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing rnaseq genesetenrichment geneexpression differentialexpression differentialsplicing immunooncology

4.38 score 12 scripts 536 downloads 18 mentions 54 exports 90 dependencies

Last updated from:e1458a799e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	207
linux-devel-x86_64	NOTE	444
source / vignettes	OK	362
linux-release-x86_64	NOTE	412
macos-release-arm64	NOTE	308
macos-oldrel-arm64	NOTE	233
windows-devel	NOTE	369
windows-release	NOTE	347
windows-oldrel	NOTE	364
wasm-release	OK	175

Exports:calES calES.perm convertEnsembl2Symbol convertSymbol2Ensembl counts counts<-DENBStat4GSEA DENBStatPermut4GSEA DENBTest DEpermutePval DSpermute4GSEA DSpermutePval DSresultExonTable DSresultGeneTable estiExonNBstat estiGeneNBstat exonID exonTestability geneID geneList genePermuteScore geneScore geneSetDescs geneSetNames geneSetSize geneTestability genpermuteMat getGeneCount GSEAresultTable GSEnrichAnalyze label loadExonCountData loadGenesets newGeneSets newReadCountSet normES normFactor plotES plotGeneScore plotSig plotSigGeneSet rankCombine runDESeq runSeqGSEA scoreNormalization signifES size subsetByGenes topDEGenes topDSExons topDSGenes topGeneSets writeScores writeSigGeneSet

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 doParallel dplyr farver fastmap filelock foreach formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gtable hms httr httr2 IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr xml2 XVector

Gene set enrichment analysis of RNA-Seq data with the SeqGSEA package

Contents

Rendered fromSeqGSEA.Rnwusingutils::Sweave

Last update: 2020-11-30
Started: 2013-11-01

Help page	Topics
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data	SeqGSEA-package SeqGSEA
Calculate running enrichment scores of gene sets	calES
Calculate enrichment scores for gene sets in the permutation data sets	calES.perm
Convert ensembl gene IDs to gene symbols	convertEnsembl2Symbol
Convert gene symbols to ensembl gene IDs	convertSymbol2Ensembl
Accessors for the 'counts' slot of a ReadCountSet object.	counts counts,ReadCountSet-method counts-methods counts<-,ReadCountSet,matrix-method
Calculate NB-statistics quantifying differential expression for each gene	DENBStat4GSEA
Calculate NB-statistics quantifying DE for each gene in the permutation data sets	DENBStatPermut4GSEA
Perform negative binomial exact test for differential expression	DENBTest
Permutation for p-values in differential expression analysis	DEpermutePval
Pre-calculated DE/DS scores	DEscore DEscore.perm DSscore DSscore.perm
Compute NB-statistics quantifying differential splicing on the permutation data set.	DSpermute4GSEA
Permutation for p-values in differential splicing analysis	DSpermutePval
Form a table for DS analysis results at the Exon level	DSresultExonTable
Form a table for DS analysis results at the gene level	DSresultGeneTable
Calculate NB-statistics quantifying differential splicing for individual exons	estiExonNBstat
Calculate NB-statistics quantifying differential splicing for each gene	estiGeneNBstat
Accessor to the exonID slot of ReadCountSet objects	exonID exonID<-
Check exon testability	exonTestability
Accessor to the geneID slot of ReadCountSet objects	geneID geneID<-
Get the gene list in a SeqGeneSet object	geneList
Calculate gene scores on permutation data sets	genePermuteScore
Calculate gene scores by integrating DE and DS scores	geneScore
Get the descriptions of gene sets in a SeqGeneSet object	geneSetDescs
Get the names of gene set in a SeqGeneSet object	geneSetNames
Get the numbers of genes in each gene set in a SeqGeneSet object	geneSetSize
Check gene testability	geneTestability
Generate permutation matrix	genpermuteMat
Calculate read counts of genes from a ReadCountSet object	getGeneCount
SeqGeneSet object example	GS_example
Form a table for GSEA results	GSEAresultTable
Main function of gene set enrichment analysis	GSEnrichAnalyze
Get the labels of samples in a ReadCountSet object	label
Load Exon Count Data	loadExonCountData
Load gene sets from files	loadGenesets
Initialize a new SeqGeneSet object	newGeneSets
Generate a new ReadCountSet object	newReadCountSet
Normalize enrichment scores	normES
Get normalization factors for normalization DE or DS scores	normFactor
Plot the distribution of enrichment scores	plotES
Plot gene (DE/DS) scores	plotGeneScore
Plot showing SeqGeneSet's p-values/FDRs vs. NESs	plotSig
Plot gene set details	plotSigGeneSet
Integration of differential expression and differential splice scores with a rank-based strategy	rankCombine
ReadCountSet object example	RCS_example
Class '"ReadCountSet"'	ReadCountSet ReadCountSet-class
Run DESeq for differential expression analysis	runDESeq
An all-in function that allows end users to apply SeqGSEA to their data with one step.	runSeqGSEA
Normalization of DE/DS scores	scoreNormalization
Class '"SeqGeneSet"'	SeqGeneSet SeqGeneSet-class show,SeqGeneSet-method [,SeqGeneSet,numeric,ANY,ANY-method [,SeqGeneSet,numeric-method
Calculate significance of ESs	signifES
Number of gene sets in a SeqGeneSet object	size
Get a new ReadCountSet with specified gene IDs.	subsetByGenes
Extract top differentially expressed genes.	topDEGenes
Extract top differentially spliced exons	topDSExons
Extract top differentially spliced genes	topDSGenes
Extract top significant gene sets	topGeneSets
Write DE/DS scores and gene scores	writeScores
Write gene set supporting information	writeSigGeneSet

Package: SeqGSEA 1.53.0

SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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