Package: SpectralTAD 1.29.0

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_1.29.0.tar.gz
SpectralTAD_1.29.0.zip(r-4.7)SpectralTAD_1.29.0.zip(r-4.6)SpectralTAD_1.29.0.zip(r-4.5)
SpectralTAD_1.29.0.tgz(r-4.6-any)SpectralTAD_1.29.0.tgz(r-4.5-any)
SpectralTAD_1.29.0.tar.gz(r-4.7-any)SpectralTAD_1.29.0.tar.gz(r-4.6-any)
SpectralTAD_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.29.0(bioc 3.24)SpectralTAD-1.28.0(bioc 3.23)

softwarehicsequencingfeatureextractionclustering

6.92 score 12 stars 28 scripts 392 downloads 5 mentions 2 exports 67 dependencies

Last updated from:a8c73aa854. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE171
linux-devel-x86_64NOTE277
source / vignettesOK290
linux-release-x86_64NOTE295
macos-release-arm64NOTE151
macos-oldrel-arm64NOTE150
windows-develNOTE167
windows-releaseNOTE173
windows-oldrelNOTE136
wasm-releaseOK135

Exports:SpectralTADSpectralTAD_Par

Dependencies:abindBHBiobaseBiocGenericsbiocmakeBiocParallelcliclustercodetoolscpp11data.tableDelayedArraydir.expirydplyrfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablegtoolsHiCcompareInteractionSetIRangesisobandKernSmoothlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmgcvnlmepheatmappillarpkgconfigPRIMMER6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector

SpectralTAD Vignette

Kellen Cresswell, John Stansfield, Mikhail Dozmorov

Rendered fromSpectralTAD.Rmdusingknitr::rmarkdownon Jun 04 2026.

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