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:Mikhail Dozmorov [aut, cre], Kellen Cresswell [aut], John Stansfield [aut]

SpectralTAD_1.23.0.tar.gz
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SpectralTAD_1.23.0.tar.gz(r-4.5-noble)SpectralTAD_1.23.0.tar.gz(r-4.4-noble)
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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

Datasets:

On BioConductor:SpectralTAD-1.23.0(bioc 3.21)SpectralTAD-1.22.0(bioc 3.20)

softwarehicsequencingfeatureextractionclustering

6.53 score 8 stars 17 scripts 294 downloads 5 mentions 2 exports 77 dependencies

Last updated 4 months agofrom:1f05a5d0e3. 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:SpectralTADSpectralTAD_Par

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigPRIMMER6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVector

SpectralTAD Vignette

Kellen Cresswell, John Stansfield, Mikhail Dozmorov

Rendered fromSpectralTAD.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2023-07-05
Started: 2019-01-30