Package: InTAD 1.32.0

Konstantin Okonechnikov

InTAD: Search for correlation between epigenetic signals and gene expression in TADs

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.

Authors:Konstantin Okonechnikov, Serap Erkek, Lukas Chavez

InTAD_1.32.0.tar.gz
InTAD_1.32.0.zip(r-4.7)InTAD_1.32.0.zip(r-4.6)InTAD_1.32.0.zip(r-4.5)
InTAD_1.32.0.tgz(r-4.6-any)InTAD_1.32.0.tgz(r-4.5-any)
InTAD_1.32.0.tar.gz(r-4.7-any)InTAD_1.32.0.tar.gz(r-4.6-any)
InTAD_1.32.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
InTAD/json (API)
NEWS

# Install 'InTAD' in R:
install.packages('InTAD', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • enhSel - Enhancer signals subset detected from medulloblatoma samples
  • enhSelGR - Genomic coordiantes of enhancer signals subet
  • loopsDfSel - Data frame containing coordinates of loops
  • mbAnnData - Data frame containing information about samples
  • rpkmCountsSel - Gene expression subset from medulloblastoma samples
  • tadGR - Genomic coordiantes of topologically associated domains
  • txsSel - Genomic coordiantes of genes subset

On BioConductor:InTAD-1.33.0(bioc 3.24)InTAD-1.32.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

epigeneticssequencingchipseqrnaseqhicgeneexpressionimmunooncology

4.48 score 9 scripts 386 downloads 2 mentions 13 exports 125 dependencies

Last updated from:129ec3db98 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR216
linux-devel-x86_64OK472
source / vignettesOK339
linux-release-x86_64OK460
macos-release-arm64OK245
macos-oldrel-arm64OK219
windows-develOK382
windows-releaseOK325
windows-oldrelOK440
wasm-releaseOK165

Exports:combineInTADcombineWithLoopsexprsfilterGeneExprfindCorFromLoopsfindCorrelationgeneCoordsloadSigInTADnewSigInTADplotCorAcrossRefplotCorrelationsigCoordssignals

Dependencies:abindaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomcarcarDatacigarilloclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDelayedArrayDerivdoBydplyrfarverforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpolynompurrrquantregqvalueR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasreshape2restfulrRhtslibrjsonrlangRsamtoolsrstatixrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXMLXVectoryamlzoo

Correlation of epigenetic signals and genes in TADs

Konstantin Okonechnikov

Rendered fromInTAD.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2020-09-06
Started: 2018-03-19