Package: SpectralTAD 1.23.0
Mikhail Dozmorov
SpectralTAD: SpectralTAD: Hierarchical TAD detection using spectral clustering
SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.
Authors:
SpectralTAD_1.23.0.tar.gz
SpectralTAD_1.23.0.zip(r-4.5)SpectralTAD_1.23.0.zip(r-4.4)SpectralTAD_1.23.0.zip(r-4.3)
SpectralTAD_1.23.0.tgz(r-4.4-any)SpectralTAD_1.23.0.tgz(r-4.3-any)
SpectralTAD_1.23.0.tar.gz(r-4.5-noble)SpectralTAD_1.23.0.tar.gz(r-4.4-noble)
SpectralTAD_1.23.0.tgz(r-4.4-emscripten)SpectralTAD_1.23.0.tgz(r-4.3-emscripten)
SpectralTAD.pdf |SpectralTAD.html✨
SpectralTAD/json (API)
NEWS
| # Install 'SpectralTAD' in R: |
| install.packages('SpectralTAD', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dozmorovlab/spectraltad/issues
- rao_chr20_25_rep - Contact matrix from Rao 2014, chromosome 20, 25kb resolution
On BioConductor:SpectralTAD-1.23.0(bioc 3.21)SpectralTAD-1.22.0(bioc 3.20)
softwarehicsequencingfeatureextractionclustering
Last updated 2 months agofrom:1f05a5d0e3. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Dec 19 2024 |
| R-4.5-linux | NOTE | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | NOTE | Dec 19 2024 |
| R-4.3-mac | NOTE | Dec 19 2024 |
Exports:SpectralTADSpectralTAD_Par
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigPRIMMER6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Contact matrix from Rao 2014, chromosome 20, 25kb resolution | rao_chr20_25_rep |
| Hierarchical Spectral Clustering of TADs | SpectralTAD |
| Parallelized Hierarchical Spectral Clustering of TADs | SpectralTAD_Par |
