Package: PAST 1.23.0

Thrash Adam

PAST: Pathway Association Study Tool (PAST)

PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.

Authors:Thrash Adam [cre, aut], DeOrnellis Mason [aut]

PAST_1.23.0.tar.gz
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PAST_1.23.0.tgz(r-4.4-any)PAST_1.23.0.tgz(r-4.3-any)
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PAST.pdf |PAST.html✨
PAST/json (API)
NEWS

# Install 'PAST' in R:
install.packages('PAST', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/igbb/past/issues

On BioConductor:PAST-1.23.0(bioc 3.21)PAST-1.22.0(bioc 3.20)

pathwaysgenesetenrichment

5.70 score 5 stars 7 scripts 196 downloads 2.3k mentions 5 exports 85 dependencies

Last updated 4 months agofrom:926ad93320. Checks:1 OK, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 23 2025
R-4.5-winWARNINGJan 23 2025
R-4.5-linuxWARNINGJan 23 2025
R-4.4-winWARNINGJan 23 2025
R-4.4-macWARNINGJan 23 2025
R-4.3-winWARNINGJan 23 2025
R-4.3-macWARNINGJan 23 2025

Exports:assign_SNPs_to_genesfind_pathway_significanceload_GWAS_dataload_LDplot_pathways

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurlDelayedArraydoParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrqvalueR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

PAST

Adam Thrash

Rendered frompast.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2020-03-11
Started: 2019-03-01