Package: Site2Target 1.5.0

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_1.5.0.tar.gz
Site2Target_1.5.0.zip(r-4.7)Site2Target_1.5.0.zip(r-4.6)Site2Target_1.5.0.zip(r-4.5)
Site2Target_1.5.0.tgz(r-4.6-any)Site2Target_1.5.0.tgz(r-4.5-any)
Site2Target_1.5.0.tar.gz(r-4.7-any)Site2Target_1.5.0.tar.gz(r-4.6-any)
Site2Target_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Site2Target/json (API)

# Install 'Site2Target' in R:

install.packages('Site2Target', repos = c('https://bioc.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)

annotation chipseq software epigenetics geneexpression genetarget

4.00 score 6 scripts 14 exports 17 dependencies

Last updated from:818ec0e19f. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	155
linux-devel-x86_64	OK	220
source / vignettes	OK	171
linux-release-x86_64	OK	179
macos-release-arm64	OK	90
macos-oldrel-arm64	OK	96
windows-devel	OK	124
windows-release	OK	108
windows-oldrel	OK	104
wasm-release	OK	108

Exports:addColumn2geneWiseAssociation addRelation2geneWiseAssociation extendSitesInGivenRegions genewiseAssociation getCenterOfPeaks getTargetGenesNumber getTargetGenesPvals getTargetGenesPvalsWithDNAInteractions getTargetGenesPvalsWithIntensities getTargetGenesPvalsWithIntensitiesAndDNAInteractions granges2String removeReserveCharacter string2Granges Table2Granges

Dependencies:askpass BiocGenerics curl generics GenomeInfoDb GenomicRanges httr IRanges jsonlite MASS mime openssl R6 S4Vectors Seqinfo sys UCSC.utils

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

Rendered fromSite2Target.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add column to gene-wise association	addColumn2geneWiseAssociation
Add a relation column to gene-peak interaction table	addRelation2geneWiseAssociation
MEIS cardiomyocytes datasets used in the package	data
Extend sites given regions boundaries	extendSitesInGivenRegions
Generate genewise association between genes and peaks	genewiseAssociation
Return center of the given granges files	getCenterOfPeaks
Get names of genes or peaks related to a query coordinates	getNameFromCoordinates
generate number of sites per gene given distances	getTargetGenesNumber
Fit Negative binomial distribution to target genes	getTargetGenesPvals
Fit Negative binomial distribution to target genes	getTargetGenesPvalsWithDNAInteractions
Fit log-normal distribution to target genes	getTargetGenesPvalsWithIntensities
Fit log-normal distribution to target genes	getTargetGenesPvalsWithIntensitiesAndDNAInteractions
Convert granges to strings of coordinates	granges2String
Remove reserved characters from a string	removeReserveCharacter
Return the distance between paired peaks and genes	site2GeneDistance
Associate peaks and target genes	Site2Target
Convert strings to granges of coordinates	string2Granges
Take Genomic Ranges from a table file	Table2Granges