Package: sevenC 1.25.0

Jonas Ibn-Salem

sevenC: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.

Authors:Jonas Ibn-Salem [aut, cre]

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NEWS

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

Peer review:

Bug tracker:https://github.com/ibn-salem/sevenc/issues

Datasets:

On BioConductor:sevenC-1.25.0(bioc 3.20)sevenC-1.24.0(bioc 3.19)

bioconductor-package

11 exports 0.82 score 76 dependencies 1 mentions

Last updated 2 months agofrom:dda512d143

Exports:addCoraddCovCoraddCovToGRaddInteractionSupportaddMotifScoreaddStrandCombinationgetCisPairsparseLoopsRaoparseLoopsTangpredLoopsprepareCisPairs

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsbootclicliprcodetoolscpp11crayoncurldata.tableDelayedArrayfansiformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehmshttrInteractionSetIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6RcppRCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLXVectoryamlzlibbioc

Prediction of chromatin looping interactions with sevenC

Jonas Ibn-Salem, Miguel Andrade-Navarro

Rendered fromsevenC.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2018-09-08
Started: 2018-01-24

Readme and manuals

Help Manual

Help pageTopics
Add correlation of ChIP-seq coverage to motif pairs.addCor
Add correlation of anchor signals to pairs of close genomic regions.addCovCor
Add coverage to regions in 'GRanges' object.addCovToGR
Add column to 'GInteractions' with overlap support.addInteractionSupport
Add motif score of anchors.addMotifScore
Add combination of anchor strand orientation.addStrandCombination
Default optimal cutoff value of logistic regression.cutoffBest10
Optimal cutoff values for logistic regression models.cutoffByTF
Build a 'GInteractions' object with all pairs of input 'GRanges' within a given distance.getCisPairs
Get out of chromosomal bound ranges.getOutOfBound
Default parameters for logistic regression model in sevenC.modelBest10Avg
CTCF motif locations in human genome hg19.motif.hg19.CTCF
CTCF motif locations on chromosome 22 in human genome hg19.motif.hg19.CTCF.chr22
CTCF motifs on human chromosome 22 with example coverage.motif.hg19.CTCF.chr22.cov
returns indices of columns with non-zero variancenoZeroVar
Parse chromatin loops from Rao et al. 2014 as strict 'GInteractions'.parseLoopsRao
Parse chromatin interactions from Tang et al. 2015 as 'GInteractions'.parseLoopsTang
Predict interaction probability using logistic regression model.predLogit
Predict looping interactions.predLoops
Prepares motif pairs as 'GInteractions' and add genomic features.prepareCisPairs
Computational chromosome conformation capture by correlation of ChIP-seq at CTCF motifs (7C)sevenC-package sevenC
Sliding mean over x of intervals of size kslideMean
TF specific parameters for logistic regression in sevenCTFspecificModels