Introduction | Getting Started | Installation | Input data | Working with $n \times n$ matrices | Working with $n \times (n+3)$ matrices | Working with sparse 3-column matrices | Working with other data types | Working with .hic files | Working with .cool files | Working with HiC-Pro files | Running SpectralTAD | Filtering TADs | Silhouette score filtering | Z-score filtering | Finding hierarchical TADS | Removing gaps | Running SpectralTAD with parallelization | Effect of matrix type on runtime | Effect of parameters on runtime | Using SpectralTAD output with HiCExplorer and Juicebox | Using SpectralTAD with HiCExplorer | Using SpectralTAD with Juicebox | References
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
SpectralTAD/json (API)
| # 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:
- rao_chr20_25_rep - Contact matrix from Rao 2014, chromosome 20, 25kb resolution
On BioConductor:SpectralTAD-1.29.0(bioc 3.24)SpectralTAD-1.28.0(bioc 3.23)
softwarehicsequencingfeatureextractionclustering
Last updated from:a8c73aa854. Checks:3 NOTE, 2 OK, 5 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 243 | ||
| linux-devel-x86_64 | NOTE | 308 | ||
| source / vignettes | OK | 347 | ||
| linux-release-x86_64 | NOTE | 323 | ||
| macos-release-arm64 | FAIL | 108 | ||
| macos-oldrel-arm64 | FAIL | 97 | ||
| windows-devel | FAIL | 93 | ||
| windows-release | FAIL | 76 | ||
| windows-oldrel | FAIL | 93 | ||
| wasm-release | OK | 242 |
Exports:SpectralTADSpectralTAD_Par
Dependencies:abindBHBiobaseBiocGenericsbiocmakeBiocParallelcliclustercodetoolscpp11data.tableDelayedArraydir.expirydplyrfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablegtoolsHiCcompareInteractionSetIRangesisobandKernSmoothlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmgcvnlmepheatmappillarpkgconfigPRIMMER6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector
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 |
