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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TADCompare/json (API)

# 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

7.15 score 27 stars 22 scripts 4 mentions 4 exports 113 dependencies

Last updated from:bd28a95824. Checks:3 NOTE, 2 OK, 5 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE277
linux-devel-x86_64NOTE340
source / vignettesOK364
linux-release-x86_64NOTE377
macos-release-arm64FAIL78
macos-oldrel-arm64FAIL76
windows-develFAIL91
windows-releaseFAIL79
windows-oldrelFAIL109
wasm-releaseOK262

Exports:ConsensusTADsDiffPlotTADCompareTimeCompare

Dependencies:abindbackportsBHBiobaseBiocGenericsbiocmakeBiocParallelbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11data.tableDelayedArrayDerivdir.expirydoBydplyrfarverfilelockforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegtoolsHiCcompareInteractionSetIRangesisobandKernSmoothlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvminqamodelrnlmenloptrnnetnumDerivpbkrtestpheatmappillarpkgconfigplyrpolynomPRIMMEpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librlangrstatixS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXVectorzoo

Gene Ontology Enrichment Analysis
Installation | Introduction | Performing gene ontology analysis using TADCompare | Session Info
Rendered fromOntology_Analysis.Rmdusingknitr::rmarkdown

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

Input data formats
Introduction | Getting Started | Installation | Working with different types of data | Working with $n \times n$ matrices | Working with $n \times (n+3)$ matrices | Working with sparse 3-column matrices | Working with other data types | Working with .hic files | Working with .cool files | Working with HiC-Pro files | Effect of matrix type on runtime | Session Info | References
Rendered fromInput_Data.Rmdusingknitr::rmarkdown

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

TAD comparison between two conditions
Installation | TADCompare | Introduction | Running TADcompare | Types of TADCompare output | Pre-specification of TADs | Visualization of TADCompare Results | Comparing TAD boundary scores | Comparing pre-defined TAD boundaries | TimeCompare | Running TimeCompare | ConsensusTAD | Running ConsensusTADs | Session Info | References
Rendered fromTADCompare.Rmdusingknitr::rmarkdown

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