Package: TADCompare 1.23.0

Mikhail Dozmorov

TADCompare: TADCompare: Identification and characterization of differential TADs

TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.

Authors:Mikhail Dozmorov [aut, cre], Kellen Cresswell [aut]

TADCompare_1.23.0.tar.gz
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TADCompare_1.23.0.tgz(r-4.6-any)TADCompare_1.23.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
TADCompare/json (API)
NEWS

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

Bug tracker:https://github.com/dozmorovlab/tadcompare/issues

Datasets:
  • GM12878.40kb.raw.chr2 - A subset of chomosome 2 contact matrix, GM12878 cell line.
  • IMR90.40kb.raw.chr2 - A subset of chomosome 2 contact matrix, IMR90 cell line.
  • rao_chr22_prim - Chromosome 22 combined intrachromosomal primary contact matrix from Rao et al. 2014.
  • rao_chr22_rep - Chromosome 22 combined intrachromosomal replicate contact matrix from Rao et al. 2014.
  • time_mats - Chromosome 22 time-varying contact matrices from Rao et al. 2017.

On BioConductor:TADCompare-1.23.0(bioc 3.24)TADCompare-1.22.0(bioc 3.23)

softwarehicsequencingfeatureextractionclustering

7.21 score 27 stars 25 scripts 448 downloads 4 mentions 4 exports 114 dependencies

Last updated from:bd28a95824. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE222
linux-devel-x86_64NOTE340
source / vignettesOK322
linux-release-x86_64NOTE326
macos-release-arm64NOTE170
macos-oldrel-arm64NOTE233
windows-develNOTE256
windows-releaseNOTE256
windows-oldrelNOTE235
wasm-releaseOK160

Exports:ConsensusTADsDiffPlotTADCompareTimeCompare

Dependencies:abindbackportsBHBiobaseBiocGenericsbiocmakeBiocParallelbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11data.tableDelayedArrayDerivdir.expirydoBydplyrfarverfilelockforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegtoolsHiCcompareInteractionSetIRangesisobandKernSmoothlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivpbkrtestpheatmappillarpkgconfigplyrpolynomPRIMMEpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librlangrstatixS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXVectorzoo

Gene Ontology Enrichment Analysis

Kellen Cresswell, Mikhail Dozmorov

Rendered fromOntology_Analysis.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-03-07
Started: 2019-09-17

Input data formats

Kellen Cresswell, Mikhail Dozmorov

Rendered fromInput_Data.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2020-04-30
Started: 2019-09-05

TAD comparison between two conditions

Kellen Cresswell, Mikhail Dozmorov

Rendered fromTADCompare.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2020-04-30
Started: 2019-08-14