Package: SpectralTAD 1.28.0

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_1.28.0.tar.gz
SpectralTAD_1.28.0.zip(r-4.7)SpectralTAD_1.28.0.zip(r-4.6)SpectralTAD_1.28.0.zip(r-4.5)
SpectralTAD_1.28.0.tgz(r-4.6-any)SpectralTAD_1.28.0.tgz(r-4.5-any)
SpectralTAD_1.28.0.tar.gz(r-4.7-any)SpectralTAD_1.28.0.tar.gz(r-4.6-any)
SpectralTAD_1.28.0.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-release.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

6.76 score 12 stars 19 scripts 426 downloads 5 mentions 2 exports 67 dependencies

Last updated from:91f40eafdf (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE162
linux-devel-x86_64NOTE266
source / vignettesOK305
linux-release-x86_64NOTE243
macos-release-arm64NOTE159
macos-oldrel-arm64NOTE154
windows-develNOTE160
windows-releaseNOTE151
windows-oldrelNOTE140
wasm-releaseOK149

Exports:SpectralTADSpectralTAD_Par

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

SpectralTAD Vignette

Kellen Cresswell, John Stansfield, Mikhail Dozmorov

Rendered fromSpectralTAD.Rmdusingknitr::rmarkdownon May 30 2026.

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