Package: loci2path 1.27.0
Tianlei Xu
loci2path: Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.
Authors:
loci2path_1.27.0.tar.gz
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loci2path.pdf |loci2path.html✨
loci2path/json (API)
NEWS
| # Install 'loci2path' in R: |
| install.packages('loci2path', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stanleyxu/loci2path/issues
On BioConductor:loci2path-1.27.0(bioc 3.21)loci2path-1.26.0(bioc 3.20)
functionalgenomicsgeneticsgenesetenrichmentsoftwaregeneexpressionsequencingcoveragebiocarta
Last updated 25 days agofrom:1995675b02. Checks:OK: 3 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win | WARNING | Nov 05 2024 |
| R-4.5-linux | WARNING | Nov 05 2024 |
| R-4.4-win | WARNING | Nov 05 2024 |
| R-4.4-mac | OK | Nov 05 2024 |
| R-4.3-win | WARNING | Nov 05 2024 |
| R-4.3-mac | OK | Nov 05 2024 |
Exports:check.geneidcoveredGenedescriptioneqtlGeneeqtlIdeqtlRangeeqtlSetgeneSetgeneSetListgetHeatmapgetMatgetPathDescriptiongetPvalgetTissueDegreegetWordcloudloci2pathResultnumGenequeryresultTabletissue
Dependencies:askpassBHBiocGenericsBiocParallelclicodetoolscolorspacecpp11curldata.tablefarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegtablehttrIRangesjsonlitelabelinglambda.rlifecyclemimemunsellopensslpheatmapR6RColorBrewerRcpprlangS4VectorsscalessnowsysUCSC.utilsviridisLitewordcloudXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| eQTL geneset enrichment query demo data | biocarta |
| check compatibility of gene identifiers between eQTL set and gene set | check.geneid |
| eqtlSet Class | eqtlGene eqtlGene,eqtlSet-method eqtlId eqtlId,eqtlSet-method eqtlRange eqtlRange,eqtlSet-method eqtlSet eqtlSet-class tissue tissue,eqtlSet-method |
| eQTL geneset enrichment query demo data | eset.list |
| geneSet Class | description description,geneSet-method geneSet geneSet-class geneSetList geneSetList,geneSet-method numGene numGene,geneSet-method |
| Generate heatmap of enrichment matrix from query result | getHeatmap getHeatmap,loci2pathResult-method |
| Extract tissue/geneset enrichment matrix from query result | getMat getMat,loci2pathResult-method |
| Extract description for enriched pathways from query result and geneSet object | getPathDescription getPathDescription,loci2pathResult-method |
| Extract tissue/geneset enrichment p-value distribution from query result | getPval getPval,loci2pathResult-method |
| Extract tissue degree from query result | getTissueDegree getTissueDegree,loci2pathResult-method |
| Plot word cloud using frequent terms of pathways and genes | getWordcloud getWordcloud,loci2pathResult-method |
| loci2pathResult Class | coveredGene coveredGene,loci2pathResult-method loci2pathResult loci2pathResult-class resultTable resultTable,loci2pathResult-method |
| Query enrichment in geneset through multiple eQTL sets. | query query,eqtlSet,geneSet-method query,GenomicRanges,eqtlSet,geneSet-method query,GenomicRanges,list,ANY-method query,GenomicRanges,list,geneSet-method query,list,geneSet-method query,list-method |
| eQTL geneset enrichment query demo data | query.gr |