Package: GSReg 1.47.0

Bahman Afsari

GSReg: Gene Set Regulation (GS-Reg)

A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).

Authors:Bahman Afsari <[email protected]>, Elana J. Fertig <[email protected]>

GSReg_1.47.0.tar.gz
GSReg_1.47.0.zip(r-4.7)GSReg_1.47.0.zip(r-4.6)GSReg_1.47.0.zip(r-4.5)
GSReg_1.47.0.tgz(r-4.6-x86_64)GSReg_1.47.0.tgz(r-4.6-arm64)GSReg_1.47.0.tgz(r-4.5-x86_64)GSReg_1.47.0.tgz(r-4.5-arm64)
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GSReg_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GSReg/json (API)

# Install 'GSReg' in R:

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

On BioConductor:GSReg-1.47.0(bioc 3.24)GSReg-1.46.0(bioc 3.23)

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

generegulation pathways geneexpression geneticvariability genesetenrichment alternativesplicing

4.06 score 19 scripts 382 downloads 3 mentions 7 exports 75 dependencies

Last updated from:8a97f7bb28. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	287
linux-devel-arm64	WARNING	319
linux-devel-x86_64	WARNING	437
source / vignettes	OK	340
linux-release-arm64	WARNING	338
linux-release-x86_64	WARNING	434
macos-release-arm64	WARNING	259
macos-release-x86_64	WARNING	541
macos-oldrel-arm64	WARNING	248
macos-oldrel-x86_64	WARNING	496
windows-devel	WARNING	432
windows-release	WARNING	289
windows-oldrel	WARNING	417
wasm-release	OK	249

Exports:GSReg.GeneSets.DIRAC GSReg.GeneSets.EVA GSReg.kendall.tau.distance GSReg.kendall.tau.distance.restricted GSReg.kendall.tau.distance.template GSReg.overlapJunction GSReg.SEVA

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue GO.db graph Homo.sapiens httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db OrganismDbi pkgconfig png R6 RBGL RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys TxDb.Hsapiens.UCSC.hg19.knownGene vctrs XML XVector yaml

Working with the GSReg package

Introduction | Input Data | Analysis of the pathways | System Information | Literature Cited

Rendered fromGSReg.Rnwusingutils::Sweave

Last update: 2018-11-16
Started: 2014-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A package for Gene Set Analysis based on the variability of gene expression in different phenotypes.	GSReg-package GSReg
Performs DIRAC for gene set analysis from the paper Eddy et al (2010).	GSReg.GeneSets.DIRAC
Performs Gene Set Analysis using Expression Variation Analysis (EVA).	GSReg.GeneSets.EVA
Calculate Kendall-tau distance in different forms	GSReg.kendall.tau.distance GSReg.kendall.tau.distance.restricted GSReg.kendall.tau.template
Generates junction overlap matrices required for SEVA	GSReg.overlapJunction
Applies Splice-EVA (SEVA) algorithm	GSReg.SEVA