Package: GOSemSim 2.39.0
Guangchuang Yu
GOSemSim: GO-terms Semantic Similarity Measures
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
Authors:
GOSemSim_2.39.0.tar.gz
GOSemSim_2.39.0.zip(r-4.7)GOSemSim_2.39.0.zip(r-4.6)GOSemSim_2.39.0.zip(r-4.5)
GOSemSim_2.39.0.tgz(r-4.6-x86_64)GOSemSim_2.39.0.tgz(r-4.6-arm64)GOSemSim_2.39.0.tgz(r-4.5-x86_64)GOSemSim_2.39.0.tgz(r-4.5-arm64)
GOSemSim_2.39.0.tar.gz(r-4.7-arm64)GOSemSim_2.39.0.tar.gz(r-4.7-x86_64)GOSemSim_2.39.0.tar.gz(r-4.6-arm64)GOSemSim_2.39.0.tar.gz(r-4.6-x86_64)
GOSemSim_2.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GOSemSim/json (API)
NEWS
| # Install 'GOSemSim' in R: |
| install.packages('GOSemSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yulab-smu/gosemsim/issues
- gotbl - Information content of GO terms
On BioConductor:GOSemSim-2.39.0(bioc 3.24)GOSemSim-2.38.0(bioc 3.23)
annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similaritycpp
Last updated from:e3e9db0789. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 216 | ||
| linux-devel-arm64 | NOTE | 281 | ||
| linux-devel-x86_64 | NOTE | 335 | ||
| source / vignettes | OK | 282 | ||
| linux-release-arm64 | NOTE | 266 | ||
| linux-release-x86_64 | NOTE | 304 | ||
| macos-release-arm64 | NOTE | 209 | ||
| macos-release-x86_64 | NOTE | 386 | ||
| macos-oldrel-arm64 | NOTE | 171 | ||
| macos-oldrel-x86_64 | NOTE | 469 | ||
| windows-devel | NOTE | 220 | ||
| windows-release | NOTE | 226 | ||
| windows-oldrel | NOTE | 216 | ||
| wasm-release | OK | 181 |
Exports:buildGOmapclusterSimcombineScoresgeneSimget_organismgodatagoSimload_OrgDbmclusterSimmgeneSimmgoSimparse_gffread.blast2goread.gaftcss_cutofftermSimwangMethod_internal
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdigestfastmapfsgenericsglueGO.dbhttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigpngR6rappdirsRcpprlangRSQLiteS4VectorsSeqinfosysvctrsXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| buildGOmap | buildGOmap |
| Semantic similarity between two gene clusters | clusterSim |
| combining similarity matrix to similarity score | combineScores |
| Semantic similarity between two genes | geneSim |
| Get organism name from OrgDb object | get_organism |
| Information content of GO terms | GO gotbl go_term_table |
| godata | godata |
| Class "GOSemSimDATA" This class stores IC and gene to go mapping for semantic similarity measurement | GOSemSimDATA-class show,GOSemSimDATA-method |
| Semantic similarity between two GO terms | goSim |
| information content based methods | infoContentMethod |
| Pairwise semantic similarities for a list of gene clusters | mclusterSim |
| Pairwise semantic similarity for a list of genes | mgeneSim |
| Semantic similarity between two GO term sets | mgoSim |
| read.blast2go | read.blast2go |
| read.gaf | parse_gff read.gaf |
| determine the topological cutoff for TCSS method | tcss_cutoff |
| termSim | termSim |
| wangMethod | wangMethod_internal |
