Package: geneAttribution 1.33.0
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:
geneAttribution_1.33.0.tar.gz
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geneAttribution.pdf |geneAttribution.html✨
geneAttribution/json (API)
NEWS
| # Install 'geneAttribution' in R: |
| install.packages('geneAttribution', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:geneAttribution-1.33.0(bioc 3.21)geneAttribution-1.32.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
snpgenepredictiongenomewideassociationvariantannotationgenomicvariation
Last updated 2 months agofrom:feca5bbac9. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | OK | Nov 29 2024 |
| R-4.5-linux | OK | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:geneAttributiongeneModelsloadBednormP
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| 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 |