Package: atacInferCnv 1.1.0

Konstantin Okonechnikov

atacInferCnv: Call CNV from single cell ATAC-seq data based on InferCNV adaptation

The package prepares input scATAC-seq data and adapts for copy number variance profiling with InferCNV package usage. It has also various paramters to control the analysis (e.g. external normal reference usage, meta-cells, bin size, etc) and custom plot visualizations.

Authors:Konstantin Okonechnikov [aut, cre], Supat Thongjuea [aut, fnd]

atacInferCnv_1.1.0.tar.gz

atacInferCnv_1.1.0.tgz(r-4.6-x86_64)atacInferCnv_1.1.0.tgz(r-4.6-arm64)atacInferCnv_1.1.0.tgz(r-4.5-x86_64)atacInferCnv_1.1.0.tgz(r-4.5-arm64)
atacInferCnv_1.1.0.tar.gz(r-4.7-arm64)atacInferCnv_1.1.0.tar.gz(r-4.7-x86_64)atacInferCnv_1.1.0.tar.gz(r-4.6-arm64)atacInferCnv_1.1.0.tar.gz(r-4.6-x86_64)
atacInferCnv_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
atacInferCnv/json (API)
NEWS

# Install 'atacInferCnv' in R:
install.packages('atacInferCnv', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kokonech/atacinfercnv/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • jags– Just Another Gibbs Sampler for Bayesian MCMC - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.

On BioConductor:atacInferCnv-1.1.0(bioc 3.24)atacInferCnv-1.0.0(bioc 3.23)

epigeneticssequencingcopynumbervariationsinglecellimmunooncologycppjags

4.85 score 3 scripts 210 downloads 3 exports 197 dependencies

Last updated from:0347acd24d. Checks:8 NOTE, 2 OK, 1 ERROR, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE285
linux-devel-arm64NOTE510
linux-devel-x86_64NOTE593
source / vignettesOK515
linux-release-arm64NOTE519
linux-release-x86_64NOTE637
macos-release-arm64NOTE350
macos-release-x86_64NOTE722
macos-oldrel-arm64NOTE372
macos-oldrel-x86_64ERROR622
windows-develFAIL387
windows-releaseFAIL369
windows-oldrelFAIL402
wasm-releaseOK227

Exports:plotCnvBlocksprepareAtacInferCnvInputrunAtacInferCnv

Dependencies:abindapeargparseaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemcaToolscliclustercodacodetoolscoincommonmarkconfigcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdoParalleldotCall64dplyrdqrngedgeRevaluatefarverfastclusterfastDummiesfastmapfastmatchfindpythonfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolshereHiddenMarkovhighrhtmltoolshtmlwidgetshttpuvhttricaigraphinfercnvIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallibcoinlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUImodeltoolsmultcompmvtnormnlmeopensslotelparallelDistparallellypatchworkpbapplyphyclustpillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppParallelRcppProgressRcppRollRcppTOMLreshape2reticulateRhtslibrjagsrlangrmarkdownROCRrprojrootRsamtoolsRSpectraRtsneS4ArraysS4VectorsS7sandwichsassscalesscattermoresctransformSeqinfoSeuratSeuratObjectshinySignacSingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsystensorTH.datatibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo

atacInferCnv: CNV inference from scATAC-seq data

Konstantin Okonechnikov

Rendered fromatacInferCnv.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-17
Started: 2026-02-05