Package: GSReg 1.39.0

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_1.39.0.tar.gz
GSReg_1.39.0.zip(r-4.5)GSReg_1.39.0.zip(r-4.4)GSReg_1.39.0.zip(r-4.3)
GSReg_1.39.0.tgz(r-4.4-arm64)GSReg_1.39.0.tgz(r-4.4-x86_64)GSReg_1.39.0.tgz(r-4.3-arm64)GSReg_1.39.0.tgz(r-4.3-x86_64)
GSReg_1.39.0.tar.gz(r-4.5-noble)GSReg_1.39.0.tar.gz(r-4.4-noble)
GSReg_1.39.0.tgz(r-4.4-emscripten)GSReg_1.39.0.tgz(r-4.3-emscripten)
GSReg.pdf |GSReg.html✨
GSReg/json (API)

# Install 'GSReg' in R:

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

Datasets:

On BioConductor:GSReg-1.39.0(bioc 3.20)GSReg-1.38.0(bioc 3.19)

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

bioconductor-package

7 exports 0.82 score 101 dependencies 3 mentions

Last updated 2 months agofrom:5f15cec76e

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 BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue GO.db graph hms Homo.sapiens httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db OrganismDbi pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RBGL RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene txdbmaker UCSC.utils utf8 vctrs withr XML xml2 XVector yaml zlibbioc

Working with the GSReg package

Rendered fromGSReg.Rnwusingutils::Sweaveon Jun 30 2024.

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).
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