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-any)goseq_1.65.0.zip(r-4.6-any)goseq_1.65.0.zip(r-4.5-any)
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

10.15 score 2 stars 10 packages 1.2k scripts 2.4k downloads 132 mentions 7 exports 88 dependencies

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

Target	Result	Time	Files	Syslog
bioc-checks	WARNING	241
linux-devel	NOTE	432
source / vignettes	OK	460
linux-release	NOTE	443
macos-release	NOTE	254
macos-oldrel	NOTE	208
windows-devel	NOTE	1125
windows-release	NOTE	1126
windows-oldrel	NOTE	982
wasm-release	OK	218

Exports:getgo getlength goseq makespline nullp plotPWF supportedOrganisms

Dependencies: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 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 memoise mgcv mime nlme openssl pillar pkgconfig png prettyunits progress purrr R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Vectors Seqinfo snow stringi stringr 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)