Package: loci2path 1.33.0

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

loci2path_1.33.0.tar.gz
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loci2path_1.33.0.tgz(r-4.6-any)loci2path_1.33.0.tgz(r-4.5-any)
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loci2path_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
loci2path/json (API)

# 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-1.33.0(bioc 3.24)loci2path-1.32.0(bioc 3.23)

functionalgenomics genetics genesetenrichment software geneexpression sequencing coverage biocarta

4.48 score 1 stars 2 scripts 2 mentions 20 exports 30 dependencies

Last updated from:ba0649606c. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	159
linux-devel-x86_64	OK	231
source / vignettes	OK	242
linux-release-x86_64	OK	248
macos-release-arm64	OK	127
macos-oldrel-arm64	OK	116
windows-devel	OK	136
windows-release	OK	159
windows-oldrel	OK	167
wasm-release	OK	135

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

Dependencies:BH BiocGenerics BiocParallel cli codetools cpp11 data.table farver formatR futile.logger futile.options generics GenomicRanges glue gtable IRanges labeling lambda.r lifecycle pheatmap R6 RColorBrewer Rcpp rlang S4Vectors scales Seqinfo snow viridisLite wordcloud

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

Rendered fromloci2path-vignette.Rmdusingknitr::rmarkdown

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