Package: deconvR 1.18.0

Irem B. Gündüz

deconvR: Simulation and Deconvolution of Omic Profiles

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

Authors:Irem B. Gündüz [aut, cre], Veronika Ebenal [aut], Altuna Akalin [aut]

deconvR_1.18.0.tar.gz
deconvR_1.18.0.zip(r-4.7)deconvR_1.18.0.zip(r-4.6)deconvR_1.18.0.zip(r-4.5)
deconvR_1.18.0.tgz(r-4.6-any)deconvR_1.18.0.tgz(r-4.5-any)
deconvR_1.18.0.tar.gz(r-4.7-any)deconvR_1.18.0.tar.gz(r-4.6-any)
deconvR_1.18.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
deconvR/json (API)
NEWS

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

Bug tracker:https://github.com/bimsbbioinfo/deconvr/issues

Datasets:

On BioConductor:deconvR-1.19.0(bioc 3.24)deconvR-1.18.0(bioc 3.23)

dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics

6.19 score 10 stars 26 scripts 460 downloads 4 exports 175 dependencies

Last updated from:7645d6ab4c (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR303
linux-devel-x86_64OK958
source / vignettesOK423
linux-release-x86_64OK914
macos-release-arm64OK628
macos-oldrel-arm64OK691
windows-develOK821
windows-releaseOK772
windows-oldrelOK761
wasm-releaseOK213

Exports:BSmeth2ProbedeconvolutefindSignaturessimulateCellMix

Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64bbmlebdsmatrixbeanplotBHBiobaseBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbootbumphuntercachemcigarilloclassclicliprcodacodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdemingDerivdigestdir.expirydoRNGdplyre1071emdbookfarverfastmapfastsegfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtablegtoolsh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmcrmemoisemethylKitmgcvmimeminfiminqamulttestmvtnormnlmenloptrnnlsnor1mixnumDerivopensslpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogressproxypurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsrobslopesRsamtoolsrsqRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryaml

deconvR : Simulation and Deconvolution of Omic Profiles

Irem B. Gunduz, Veronika Ebenal, Altuna Akalin

Rendered fromdeconvRVignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-12-03
Started: 2021-10-11