Package: goseq 1.65.0

Federico Marini

goseq: Gene Ontology analyser for RNA-seq and other length biased data

Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

Authors:Matthew Young [aut], Nadia Davidson [aut], Federico Marini [ctb, cre]

goseq_1.65.0.tar.gz
goseq_1.65.0.zip(r-4.7)goseq_1.65.0.zip(r-4.6)goseq_1.65.0.zip(r-4.5)
goseq_1.65.0.tgz(r-4.6-any)goseq_1.65.0.tgz(r-4.5-any)
goseq_1.65.0.tar.gz(r-4.7-any)goseq_1.65.0.tar.gz(r-4.6-any)
goseq_1.65.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
goseq/json (API)

# Install 'goseq' in R:

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

Bug tracker:https://github.com/federicomarini/goseq/issues

Datasets:

genes - Androgen stimulation of prostate cancer Cell lines.

On BioConductor:goseq-1.65.0(bioc 3.24)goseq-1.64.0(bioc 3.23)

immunooncology sequencing go geneexpression transcription rnaseq differentialexpression annotation genesetenrichment kegg pathways software

9.87 score 2 stars 10 packages 1.0k scripts 132 mentions 7 exports 96 dependencies

Last updated from:8a3353bee0. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	WARNING	270
linux-devel-x86_64	NOTE	469
source / vignettes	OK	458
linux-release-x86_64	NOTE	442
macos-release-arm64	NOTE	298
macos-oldrel-arm64	NOTE	223
windows-devel	NOTE	1236
windows-release	NOTE	1207
windows-oldrel	NOTE	1000
wasm-release	OK	228

Exports:getgo getlength goseq makespline nullp plotPWF supportedOrganisms

Dependencies:abind AnnotationDbi askpass BH BiasedUrn Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr fastmap filelock formatR futile.logger futile.options geneLenDataBase generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue GO.db hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs withr XML xml2 XVector yaml

goseq User's Guide

Rendered fromgoseq.Rnwusingutils::Sweave

Last update: 2024-06-12
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Androgen stimulation of prostate cancer Cell lines.	genes
Fetch GO categories	getgo
Retrieves Gene length data	getlength
goseq Gene Ontology analyser	goseq
Monotonic Spline	makespline
Probability Weighting Function	nullp
Plot the Probability Weighting Function	plotPWF
Prints progress through a loop	pp
Supported Organisms	supportedOrganisms

Usage by other packages (reverse dependencies)