Introduction | Installing betterChromVAR | Computing motif deviations with betterChromVAR | Individual steps of betterChromVAR | Including fragment length bias | Note on single-cell data | Execution on Atlas-scale datasets | Motif variability and reliability | Smoothing the deviations of single cells across neighboring cells | Bias-normalization of bulk ATAC-seq data | betterChromVAR with kNN-based background | Appendix | References | Session info
Package: betterChromVAR 1.1.12
Pierre-Luc Germain
betterChromVAR: Improved ChromVAR (Chromatin Variation Across Regions)
A much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.
Authors:
betterChromVAR_1.1.12.tar.gz
betterChromVAR_1.1.12.zip(r-4.7-any)betterChromVAR_1.1.12.zip(r-4.6-any)betterChromVAR_1.1.12.zip(r-4.5-any)
betterChromVAR_1.1.12.tgz(r-4.6-any)betterChromVAR_1.1.12.tgz(r-4.5-any)
betterChromVAR_1.1.12.tar.gz(r-4.7-any)betterChromVAR_1.1.12.tar.gz(r-4.6-any)
betterChromVAR_1.1.12.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
betterChromVAR/json (API)
| # Install 'betterChromVAR' in R: |
| install.packages('betterChromVAR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/plger/betterchromvar/issues
On BioConductor:betterChromVAR-1.1.10(bioc 3.24)betterChromVAR-1.0.3(bioc 3.23)
softwareatacseqnormalizationepigeneticssequencing
Last updated from:d64e3b5d0f. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 333 | ||
| linux-devel | NOTE | 460 | ||
| source / vignettes | OK | 347 | ||
| linux-release | NOTE | 535 | ||
| macos-release | NOTE | 265 | ||
| macos-oldrel | NOTE | 212 | ||
| windows-devel | NOTE | 273 | ||
| windows-release | NOTE | 542 | ||
| windows-oldrel | NOTE | 264 | ||
| wasm-release | OK | 213 |
Exports:addGCBiasbetterChromVARcomputeBackgroundscomputeDeviationsAnalyticcomputeDeviationsFromKNNcomputeDeviationsWeightedcomputeMotifReliabilitycomputeMotifVariabilityCVnormestimateNoiseKappagetBackgroundBinsgetBackgroundKNNgetDummyDatagetExpectationnormalizeDevsForSizesampleBackgroundPeaksshowshrinkColumnPropssmoothDeviationsKNN
Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiostringscodetoolscpp11crayonDelayedArrayDelayedMatrixStatsformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSeqinfosnowSparseArraysparseMatrixStatsSummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| addGCBias | addGCBias |
| Coerce bcvBackground to a list | as.list,bcvBackground-method show,bcvBackground-method [,bcvBackground,ANY,ANY,ANY-method |
| Bin and background data for betterChromVAR (for internal use) | bcvBackground-class |
| betterChromVAR | betterChromVAR |
| computeBackgrounds | computeBackgrounds |
| computeDeviationsAnalytic | computeDeviationsAnalytic |
| computeDeviationsFromKNNbg | computeDeviationsFromKNN |
| computeDeviationsWeighted | computeDeviationsWeighted |
| computeMotifReliability | computeMotifReliability |
| computeMotifVariability | computeMotifVariability |
| CVnorm: chromVAR-inspired ATAC-seq normalization | CVnorm |
| estimateNoiseKappa | estimateNoiseKappa |
| getBackgroundBins | getBackgroundBins |
| getBackgroundKNN | getBackgroundKNN |
| Dummy data for testing purposes | getDummyData |
| getExpectation | getExpectation |
| normalizeDevsForSize | normalizeDevsForSize |
| sampleBackgroundPeaks | sampleBackgroundPeaks |
| shrinkColumnProps | shrinkColumnProps |
| smoothDeviationsKNN | smoothDeviationsKNN |