Vignette | Citation | Need helps?
Package: GOSemSim 2.39.2
Guangchuang Yu
GOSemSim: GO-terms Semantic Similarity Measures
Semantic similarity analysis of Gene Ontology (GO) annotations provides a quantitative framework for comparing GO terms, gene products, and gene clusters. GOSemSim implements widely used information content- and graph-based similarity measures, including the methods of Resnik, Schlicker, Jiang, Lin, Wang and TCSS. It also provides utilities for preparing annotation data and combining term-level similarities into gene- and cluster-level scores.
Authors:
GOSemSim_2.39.2.tar.gz
GOSemSim_2.39.2.zip(r-4.7)GOSemSim_2.39.2.zip(r-4.6)GOSemSim_2.39.2.zip(r-4.5)
GOSemSim_2.39.2.tgz(r-4.6-x86_64)GOSemSim_2.39.2.tgz(r-4.6-arm64)GOSemSim_2.39.2.tgz(r-4.5-x86_64)GOSemSim_2.39.2.tgz(r-4.5-arm64)
GOSemSim_2.39.2.tar.gz(r-4.7-arm64)GOSemSim_2.39.2.tar.gz(r-4.7-x86_64)GOSemSim_2.39.2.tar.gz(r-4.6-arm64)GOSemSim_2.39.2.tar.gz(r-4.6-x86_64)
GOSemSim_2.39.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GOSemSim/json (API)
| # 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
Datasets:
- gotbl - Information content of GO terms
On BioConductor:GOSemSim-2.39.0(bioc 3.24)GOSemSim-2.38.0(bioc 3.23)
annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similarityquartocpp
Last updated from:e6caf6daa6. Checks:1 ERROR, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 229 | ||
| linux-devel-arm64 | OK | 417 | ||
| linux-devel-x86_64 | OK | 481 | ||
| source / vignettes | OK | 359 | ||
| linux-release-arm64 | OK | 414 | ||
| linux-release-x86_64 | OK | 460 | ||
| macos-release-arm64 | OK | 333 | ||
| macos-release-x86_64 | OK | 654 | ||
| macos-oldrel-arm64 | OK | 338 | ||
| macos-oldrel-x86_64 | OK | 531 | ||
| windows-devel | OK | 434 | ||
| windows-release | OK | 437 | ||
| windows-oldrel | OK | 423 | ||
| wasm-release | OK | 219 |
Exports:buildGOmapclusterSimcombineScoresgeneSimget_organismgodatagoSimload_OrgDbmclusterSimmgeneSimmgoSimparse_gffread.blast2goread.gafset_auto_updatetcss_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 |
| Control auto-update of ontology databases | set_auto_update |
| determine the topological cutoff for TCSS method | tcss_cutoff |
| termSim | termSim |
| wangMethod | wangMethod_internal |
