Loading GWAS Data | Loading LD Data | Assigning SNPs to Genes | Finding Pathway Significance | Plotting Selected Pathways | References
Package: PAST 1.29.0
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:
PAST_1.29.0.tar.gz
PAST_1.29.0.zip(r-4.7)PAST_1.29.0.zip(r-4.6)PAST_1.29.0.zip(r-4.5)
PAST_1.29.0.tgz(r-4.6-any)PAST_1.29.0.tgz(r-4.5-any)
PAST_1.29.0.tar.gz(r-4.7-any)PAST_1.29.0.tar.gz(r-4.6-any)
PAST_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PAST/json (API)
| # 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-1.29.0(bioc 3.24)PAST-1.28.0(bioc 3.23)
Last updated from:b3a609543d. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 197 | ||
| linux-devel-x86_64 | WARNING | 520 | ||
| source / vignettes | OK | 312 | ||
| linux-release-x86_64 | WARNING | 539 | ||
| macos-release-arm64 | WARNING | 287 | ||
| macos-oldrel-arm64 | WARNING | 244 | ||
| windows-devel | WARNING | 406 | ||
| windows-release | WARNING | 430 | ||
| windows-oldrel | WARNING | 324 | ||
| wasm-release | OK | 199 |
Exports:assign_SNPs_to_genesfind_pathway_significanceload_GWAS_dataload_LDplot_pathways
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurlDelayedArraydoParalleldplyrfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrqvalueR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectutf8vctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assign SNPs in a chunk to genes | assign_chunk |
| Assign SNPs to genes | assign_SNPs_to_genes |
| Determine Linkage | determine_linkage |
| Find Pathway Significance | find_pathway_significance |
| Find representative SNP for a chunk of SNPs | find_representative_SNP |
| Find the SNP-gene assignment that represents SNPs assigned to a gene | find_representative_SNP_gene_pairing |
| Load GWAS data | load_GWAS_data |
| Load Linkage Disequilibrium | load_LD |
| Plot Rugplots for Selected Pathways | plot_pathways |
