Package: loci2path 1.25.0

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:Tianlei Xu

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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

Datasets:

biocarta - EQTL geneset enrichment query demo data
eset.list - EQTL geneset enrichment query demo data
query.gr - EQTL geneset enrichment query demo data

On BioConductor:loci2path-1.25.0(bioc 3.20)loci2path-1.24.0(bioc 3.19)

bioconductor-package

20 exports 1.31 score 42 dependencies 2 mentions

Last updated 2 months agofrom:c307a2091f

Exports:check.geneid coveredGene description eqtlGene eqtlId eqtlRange eqtlSet geneSet geneSetList getHeatmap getMat getPathDescription getPval getTissueDegree getWordcloud loci2pathResult numGene query resultTable tissue

Dependencies:askpass BH BiocGenerics BiocParallel cli codetools colorspace cpp11 curl data.table farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges glue gtable httr IRanges jsonlite labeling lambda.r lifecycle mime munsell openssl pheatmap R6 RColorBrewer Rcpp rlang S4Vectors scales snow sys UCSC.utils viridisLite wordcloud XVector zlibbioc

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Tianlei Xu

Rendered fromloci2path-vignette.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2018-01-22
Started: 2017-08-19

Citation

Development and contributors

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