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

InTAD_1.27.0.tar.gz
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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'))

Peer review:

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 7 scripts 196 downloads 2 mentions 13 exports 118 dependencies

Last updated 2 months agofrom:4f6fc186bd. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:combineInTADcombineWithLoopsexprsfilterGeneExprfindCorFromLoopsfindCorrelationgeneCoordsloadSigInTADnewSigInTADplotCorAcrossRefplotCorrelationsigCoordssignals

Dependencies:abindaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDelayedArrayDerivdoBydplyrfansifarverformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpolynompurrrquantregqvalueR6RColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrstatixrtracklayerS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

Correlation of epigenetic signals and genes in TADs

Konstantin Okonechnikov

Rendered fromInTAD.Rmdusingknitr::rmarkdownon Nov 29 2024.

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