Introduction | Installation | Quick start | From OrthoFinder results | Session Info
Package: geneClusterPattern 0.99.2
Jianhong Ou
geneClusterPattern: Plot conserved gene pattern across multiple species
An R package for constructing and comparing ortholog gene patterns around a focal gene across species. It enables the exploration of conserved gene neighborhoods (synteny) by organizing orthologous genes within a defined genomic window and aligning their relative positions across multiple genomes. It can retrieve homologous gene directly from Ensembl or it can incorporate user-provided ortholog group assignments.
Authors:
geneClusterPattern_0.99.2.tar.gz
geneClusterPattern_0.99.2.zip(r-4.7-any)geneClusterPattern_0.99.2.zip(r-4.6-any)geneClusterPattern_0.99.2.zip(r-4.5-any)
geneClusterPattern_0.99.2.tgz(r-4.6-any)geneClusterPattern_0.99.2.tgz(r-4.5-any)
geneClusterPattern_0.99.2.tar.gz(r-4.7-any)geneClusterPattern_0.99.2.tar.gz(r-4.6-any)
geneClusterPattern_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geneClusterPattern/json (API)
| # Install 'geneClusterPattern' in R: |
| install.packages('geneClusterPattern', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jianhong/geneclusterpattern/issues
On BioConductor:geneClusterPattern-0.99.2(bioc 3.24)
Last updated from:a879182eb1. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 225 | ||
| linux-devel | OK | 475 | ||
| source / vignettes | OK | 361 | ||
| linux-release | OK | 419 | ||
| macos-release | OK | 332 | ||
| macos-oldrel | OK | 325 | ||
| windows-devel | OK | 387 | ||
| windows-release | OK | 361 | ||
| windows-oldrel | OK | 393 | ||
| wasm-release | OK | 199 |
Exports:fromOrthogroupsgeneOrderScoregetGeneClustergetGeneRankgetHomologGeneListgetHomologListForOrthoFindergrangesFromEnsemblIDsguessSpecieshomologsFromEnsemblIDsorthologPairsFromOrthoFinderplotGeneClusterPatternspruningSequences
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdir.expirydplyrevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluegrImporthighrhmshtmltoolshtmlwidgetshttrhttr2InteractionSetIRangesjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrpwalignR6RANNrappdirsRColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesSeqinfosnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextrackViewertxdbmakerUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot conserved gene pattern cross multiple species | geneClusterPattern-package geneClusterPattern |
| Read Orthologues results as a list This function is under-development. | fromOrthogroups |
| Calculate the gene order score | geneOrderScore |
| calculate the gene cluster | getGeneCluster |
| Get the gene position orders | getGeneRank |
| Get the gene positions for homologs | getHomologGeneList |
| Get the gene position orders for output of OrthoFinder | getHomologListForOrthoFinder |
| create a GRanges object by given ensembl gene ids | grangesFromEnsemblIDs |
| Guess the species | guessSpecies |
| retrieve a homologs by given ensembl gene ids | homologsFromEnsemblIDs |
| Read orthoFinder Orthologues results as a list Read orthoFinder Orthologues results as a list for each pair of orthologs. | orthologPairsFromOrthoFinder |
| plot gene patters for given ids | plotGeneClusterPatterns |
| Drop non-standard chromosomes Remove the unwanted chromosomes from a list of GRanges object. | pruningSequences |