Package: Site2Target 1.4.0

Peyman Zarrineh

Site2Target: An R package to associate peaks and target genes

Statistics implemented for both peak-wise and gene-wise associations. In peak-wise associations, the p-value of the target genes of a given set of peaks are calculated. Negative binomial or Poisson distributions can be used for modeling the unweighted peaks targets and log-nromal can be used to model the weighted peaks. In gene-wise associations a table consisting of a set of genes, mapped to specific peaks, is generated using the given rules.

Authors:Peyman Zarrineh [cre, aut]

Site2Target_1.4.0.tar.gz
Site2Target_1.4.0.zip(r-4.7)Site2Target_1.4.0.zip(r-4.6)Site2Target_1.4.0.zip(r-4.5)
Site2Target_1.4.0.tgz(r-4.6-any)Site2Target_1.4.0.tgz(r-4.5-any)
Site2Target_1.4.0.tar.gz(r-4.7-any)Site2Target_1.4.0.tar.gz(r-4.6-any)
Site2Target_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Site2Target/json (API)
NEWS

# Install 'Site2Target' in R:
install.packages('Site2Target', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fls-bioinformatics-core/site2target/issues

On BioConductor:Site2Target-1.5.0(bioc 3.24)Site2Target-1.4.0(bioc 3.23)

annotationchipseqsoftwareepigeneticsgeneexpressiongenetarget

4.00 score 6 scripts 220 downloads 14 exports 17 dependencies

Last updated from:ce9001280a (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE145
linux-devel-x86_64OK215
source / vignettesOK184
linux-release-x86_64OK182
macos-release-arm64OK121
macos-oldrel-arm64OK131
windows-develOK117
windows-releaseOK81
windows-oldrelOK102
wasm-releaseOK110

Exports:addColumn2geneWiseAssociationaddRelation2geneWiseAssociationextendSitesInGivenRegionsgenewiseAssociationgetCenterOfPeaksgetTargetGenesNumbergetTargetGenesPvalsgetTargetGenesPvalsWithDNAInteractionsgetTargetGenesPvalsWithIntensitiesgetTargetGenesPvalsWithIntensitiesAndDNAInteractionsgranges2StringremoveReserveCharacterstring2GrangesTable2Granges

Dependencies:askpassBiocGenericscurlgenericsGenomeInfoDbGenomicRangeshttrIRangesjsonliteMASSmimeopensslR6S4VectorsSeqinfosysUCSC.utils

'Site2Target': an R package to associate peaks and target genes

Peyman Zarrineh

Rendered fromSite2Target.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-01-15
Started: 2024-10-12