Package: InTAD 1.27.0

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

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InTAD.pdf |InTAD.html✨
InTAD/json (API)
NEWS

# Install 'InTAD' in R:
install.packages('InTAD', repos = c('https://bioc.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-1.27.0(bioc 3.21)InTAD-1.26.0(bioc 3.20)

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

epigeneticssequencingchipseqrnaseqhicgeneexpressionimmunooncology

4.30 score 6 scripts 232 downloads 2 mentions 13 exports 120 dependencies

Last updated 4 months agofrom:4f6fc186bd. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winOKJan 28 2025
R-4.5-macOKJan 28 2025
R-4.5-linuxOKJan 28 2025
R-4.4-winOKJan 28 2025
R-4.4-macOKJan 28 2025
R-4.3-winOKJan 28 2025
R-4.3-macOKJan 28 2025

Exports:combineInTADcombineWithLoopsexprsfilterGeneExprfindCorFromLoopsfindCorrelationgeneCoordsloadSigInTADnewSigInTADplotCorAcrossRefplotCorrelationsigCoordssignals

Dependencies:abindaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDelayedArrayDerivdoBydplyrfansifarverformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpolynompurrrquantregqvalueR6rbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasreshape2restfulrRhtslibrjsonrlangRsamtoolsrstatixrtracklayerS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Correlation of epigenetic signals and genes in TADs

Konstantin Okonechnikov

Rendered fromInTAD.Rmdusingknitr::rmarkdownon Jan 28 2025.

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