Package: geneAttribution 1.39.0

Arthur Wuster

geneAttribution: Identification of candidate genes associated with genetic variation

Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.

Authors:Arthur Wuster

geneAttribution_1.39.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geneAttribution/json (API)

# Install 'geneAttribution' in R:

install.packages('geneAttribution', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:geneAttribution-1.39.0(bioc 3.24)geneAttribution-1.38.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

snp geneprediction genomewideassociation variantannotation genomicvariation

4.18 score 3 scripts 1 mentions 4 exports 68 dependencies

Last updated from:1ad1d6c7e1. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	278
linux-devel-x86_64	WARNING	451
source / vignettes	OK	350
linux-release-x86_64	WARNING	456
macos-release-arm64	WARNING	268
macos-oldrel-arm64	WARNING	225
windows-devel	WARNING	340
windows-release	WARNING	341
windows-oldrel	WARNING	295
wasm-release	OK	222

Exports:geneAttribution geneModels loadBed normP

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db pkgconfig png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys vctrs XML XVector yaml

geneAttribution: Identification of Candidate Genes Associated with Noncoding Genetic Variation

Basic functionality | geneModels() | geneAttribution() | Using empirical data | Obtaining the coordinates of candidate genes

Rendered fromgeneAttribution.Rmdusingknitr::rmarkdown

Last update: 2016-10-07
Started: 2016-08-26

Help page	Topics
geneAttribution: Identification of candidate genes associated with noncoding genetic variation	geneAttribution-package geneAttribution
Load gene models	geneModels
Load UCSC *.BED files containing empirical data	loadBed
Normalize likelihoods and return probabilities	normP

Package: geneAttribution 1.39.0

geneAttribution: Identification of candidate genes associated with genetic variation

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Help Manual

Usage by other packages (reverse dependencies)