Introduction | Function Overview | Parameters | Return Value | Usage Examples | How It Works | The Measure of Concordance (MoC) Score | Dynamic Programming for Optimal TAD Selection | Important Notes
Package: consensusTADs 0.99.4
Pumin Li
consensusTADs: Generate Consensus Topologically Associating Domains from Multiple Prediction Tools
Integrates Topologically Associating Domains (TADs) predictions from multiple computational tools to generate high-confidence consensus TAD sets. The package implements the Measure of Concordance (MoC) metric to quantify agreement between different TAD predictions and uses dynamic programming algorithms to select optimal non-overlapping TAD boundaries. This approach helps resolve inconsistencies between TAD calling methods and produces more reliable chromatin domain annotations for downstream genomic analyses.
Authors:
consensusTADs_0.99.4.tar.gz
consensusTADs_0.99.4.zip(r-4.7-any)consensusTADs_0.99.4.zip(r-4.6-any)consensusTADs_0.99.4.zip(r-4.5-any)
consensusTADs_0.99.4.tgz(r-4.6-any)consensusTADs_0.99.4.tgz(r-4.5-any)
consensusTADs_0.99.4.tar.gz(r-4.7-any)consensusTADs_0.99.4.tar.gz(r-4.6-any)
consensusTADs_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
consensusTADs/json (API)
| # Install 'consensusTADs' in R: |
| install.packages('consensusTADs', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/csogroup/consensustads/issues
Last updated from:708b0091f2. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 174 | ||
| linux-devel | NOTE | 202 | ||
| source / vignettes | OK | 212 | ||
| linux-release | NOTE | 196 | ||
| macos-release | NOTE | 133 | ||
| macos-oldrel | NOTE | 138 | ||
| windows-devel | NOTE | 124 | ||
| windows-release | NOTE | 127 | ||
| windows-oldrel | NOTE | 157 | ||
| wasm-release | OK | 129 |
Exports:generate_tad_consensusgenerate_tad_consensus_hierarchymoc_score_filterselect_global_optimal_tadsselect_tads_by_thresholdselect_tads_by_threshold_series
Dependencies:BiocGenericsclicodetoolscpp11digestdplyrfurrrfuturegenericsGenomicRangesglobalsglueIRangeslifecyclelistenvmagrittrparallellypillarpkgconfigpurrrR6rlangS4VectorsSeqinfostringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generate consensus TADs from multiple tool predictions | generate_tad_consensus |
| Generate hierarchical consensus TADs through iterative rounds | generate_tad_consensus_hierarchy |
| Calculate and filter Measure of Concordance (MoC) between TADs | moc_score_filter |
| Select globally optimal non-overlapping TADs using dynamic programming | select_global_optimal_tads |
| Select optimal non-overlapping TADs using a single threshold | select_tads_by_threshold |
| Select TADs using a series of decreasing thresholds | select_tads_by_threshold_series |