Package: TADCompare 1.17.0

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_1.17.0.tar.gz
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TADCompare.pdf |TADCompare.html✨
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-1.17.0(bioc 3.21)TADCompare-1.16.0(bioc 3.20)

softwarehicsequencingfeatureextractionclustering

7.04 score 23 stars 10 scripts 260 downloads 4 mentions 4 exports 115 dependencies

Last updated 4 months agofrom:e550de3041. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winNOTEFeb 17 2025
R-4.5-macNOTEFeb 17 2025
R-4.5-linuxNOTEFeb 17 2025
R-4.4-winNOTEFeb 17 2025
R-4.4-macNOTEFeb 17 2025
R-4.3-winNOTEFeb 17 2025
R-4.3-macNOTEFeb 17 2025

Exports:ConsensusTADsDiffPlotTADCompareTimeCompare

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdoBydplyrfansifarverformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpheatmappillarpkgconfigplyrpolynomPRIMMEpurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librlangrstatixS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVector

Gene Ontology Enrichment Analysis

Kellen Cresswell, Mikhail Dozmorov

Rendered fromOntology_Analysis.Rmdusingknitr::rmarkdownon Feb 17 2025.

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

Input data formats

Kellen Cresswell, Mikhail Dozmorov

Rendered fromInput_Data.Rmdusingknitr::rmarkdownon Feb 17 2025.

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

TAD comparison between two conditions

Kellen Cresswell, Mikhail Dozmorov

Rendered fromTADCompare.Rmdusingknitr::rmarkdownon Feb 17 2025.

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