Package: TADCompare 1.15.0
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:
TADCompare_1.15.0.tar.gz
TADCompare_1.15.0.zip(r-4.5)TADCompare_1.15.0.zip(r-4.4)TADCompare_1.15.0.zip(r-4.3)
TADCompare_1.15.0.tgz(r-4.4-any)TADCompare_1.15.0.tgz(r-4.3-any)
TADCompare_1.15.0.tar.gz(r-4.5-noble)TADCompare_1.15.0.tar.gz(r-4.4-noble)
TADCompare_1.15.0.tgz(r-4.4-emscripten)TADCompare_1.15.0.tgz(r-4.3-emscripten)
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
- 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-1.15.0(bioc 3.20)TADCompare-1.14.0(bioc 3.19)
Last updated 2 months agofrom:40787bdf57
Exports:ConsensusTADsDiffPlotTADCompareTimeCompare
Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelbootbriobroomcallrcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDelayedArraydescdiffobjdigestdplyrevaluatefansifarverformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmimeminqamunsellnlmenloptrnnetnumDerivopensslpbkrtestpheatmappillarpkgbuildpkgconfigpkgloadplyrpolynompraisePRIMMEprocessxpspurrrquantregR6RColorBrewerRcppRcppEigenrematch2reshape2rhdf5rhdf5filtersRhdf5librlangrprojrootrstatixS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystestthattibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewaldowithrXVectorzlibbioc
Gene Ontology Enrichment Analysis
Rendered fromOntology_Analysis.Rmdusingknitr::rmarkdownon Jun 17 2024.Last update: 2024-03-07
Started: 2019-09-17
Input data formats
Rendered fromInput_Data.Rmdusingknitr::rmarkdownon Jun 17 2024.Last update: 2020-04-30
Started: 2019-09-05
TAD comparison between two conditions
Rendered fromTADCompare.Rmdusingknitr::rmarkdownon Jun 17 2024.Last update: 2020-04-30
Started: 2019-08-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Consensus boundary identification | ConsensusTADs |
| Visualization of differential TAD boundaries | DiffPlot |
| A subset of chomosome 2 contact matrix, GM12878 cell line. | GM12878.40kb.raw.chr2 |
| A subset of chomosome 2 contact matrix, IMR90 cell line. | IMR90.40kb.raw.chr2 |
| Chromosome 22 combined intrachromosomal primary contact matrix from Rao et al. 2014. | rao_chr22_prim |
| Chromosome 22 combined intrachromosomal replicate contact matrix from Rao et al. 2014. | rao_chr22_rep |
| Differential TAD boundary detection | TADCompare |
| Chromosome 22 time-varying contact matrices from Rao et al. 2017. | time_mats |
| Time-varying TAD boundary analysis | TimeCompare |
