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]

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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'))

Peer review:

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 9 scripts 238 downloads 4 mentions 4 exports 113 dependencies

Last updated 2 months agofrom:e550de3041. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winNOTEDec 19 2024
R-4.3-macNOTEDec 19 2024

Exports:ConsensusTADsDiffPlotTADCompareTimeCompare

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdoBydplyrfansifarverformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpheatmappillarpkgconfigplyrpolynomPRIMMEpurrrquantregR6RColorBrewerRcppRcppEigenreshape2rhdf5rhdf5filtersRhdf5librlangrstatixS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Gene Ontology Enrichment Analysis

Kellen Cresswell, Mikhail Dozmorov

Rendered fromOntology_Analysis.Rmdusingknitr::rmarkdownon Dec 19 2024.

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

Input data formats

Kellen Cresswell, Mikhail Dozmorov

Rendered fromInput_Data.Rmdusingknitr::rmarkdownon Dec 19 2024.

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

TAD comparison between two conditions

Kellen Cresswell, Mikhail Dozmorov

Rendered fromTADCompare.Rmdusingknitr::rmarkdownon Dec 19 2024.

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