Package: goseq 1.64.0

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_1.64.0.tar.gz
goseq_1.64.0.zip(r-4.7)goseq_1.64.0.zip(r-4.6)goseq_1.64.0.zip(r-4.5)
goseq_1.64.0.tgz(r-4.6-any)goseq_1.64.0.tgz(r-4.5-any)
goseq_1.64.0.tar.gz(r-4.7-any)goseq_1.64.0.tar.gz(r-4.6-any)
goseq_1.64.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
goseq/json (API)
NEWS

# Install 'goseq' in R:

install.packages('goseq', repos = c('https://bioc-release.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

9.13 score 2 stars 10 packages 760 scripts 2.5k downloads 132 mentions 7 exports 95 dependencies

Last updated from:659e2a1a39 (on RELEASE_3_23). Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: no.

Target	Result	Time	Files	Syslog
bioc-checks	WARNING	258
linux-devel-x86_64	ERROR	459
source / vignettes	ERROR	369
linux-release-x86_64	ERROR	450
macos-release-arm64	ERROR	275
macos-oldrel-arm64	ERROR	247
windows-devel	ERROR	1293
windows-release	ERROR	966
windows-oldrel	ERROR	976
wasm-release	OK	227

Exports:getgo getlength goseq makespline nullp plotPWF supportedOrganisms

Dependencies:abind AnnotationDbi askpass BH BiasedUrn Biobase 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

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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)