Package: vmrseq 1.5.0

Ning Shen

vmrseq: Probabilistic Modeling of Single-cell Methylation Heterogeneity

High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. We present vmrseq, a statistical method that overcomes these challenges and identifies variably methylated regions accurately and robustly.

Authors:Ning Shen [aut, cre]

vmrseq_1.5.0.tar.gz
vmrseq_1.5.0.zip(r-4.7)vmrseq_1.5.0.zip(r-4.6)vmrseq_1.5.0.zip(r-4.5)
vmrseq_1.5.0.tgz(r-4.6-any)vmrseq_1.5.0.tgz(r-4.5-any)
vmrseq_1.5.0.tar.gz(r-4.7-any)vmrseq_1.5.0.tar.gz(r-4.6-any)
vmrseq_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
vmrseq/json (API)

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

Bug tracker:https://github.com/nshen7/vmrseq/issues

Datasets:

On BioConductor:vmrseq-1.5.0(bioc 3.24)vmrseq-1.4.0(bioc 3.23)

softwareimmunooncologydnamethylationepigeneticssinglecellsequencingwholegenomecomputational-biologydimensionality-reductionepigenomics-workflowhidden-markov-modelprobabilistic-models

4.18 score 10 stars 5 scripts 8 exports 181 dependencies

Last updated from:350bbc11e7. Checks:1 NOTE, 8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE235
linux-devel-x86_64ERROR426
source / vignettesERROR356
linux-release-x86_64ERROR444
macos-release-arm64ERROR250
macos-oldrel-arm64ERROR237
windows-develERROR364
windows-releaseERROR397
windows-oldrelERROR400
wasm-releaseOK244

Exports:HDF5NAdrop2matrixpoolDataregionSummarytpEstimatetpPlotvmrseqFitvmrseqOptimControlvmrseqSmooth

Dependencies:abindAnnotationDbiarulesaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbrewbriobslibbumphuntercachemcallrcigarilloclicliprcodetoolscommonmarkcpp11crayoncredentialscurldata.tableDBIDelayedArraydescdevtoolsdiffobjdigestdir.expirydoRNGdownlitdplyrellipsisevaluatefansifarverfastmapfilelockfloatfontawesomeforeachformatRfsfutile.loggerfutile.optionsgamlss.distgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgertggplot2gitcredsgluegtableh5mreadHDF5Arrayhighrhtmltoolshtmlwidgetshttpuvhttrhttr2iniIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIopensslotelpakpillarpkgbuildpkgconfigpkgdownpkgloadpngpraiseprettyunitsprocessxprofvispromisesproxypspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRcppProgressRCurlrecommenderlabrecosystemregistryrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsroxygen2rprojrootRsamtoolsRSQLiterstudioapirtracklayerrversionsS4ArraysS4VectorsS7sassscalesSeqinfosessioninfoshinysnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstestthattextshapingtibbletidyrtidyselecttinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunXMLxml2xopenxtableXVectoryamlzip