Package: deconvR 1.13.0

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]

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deconvR.pdf |deconvR.html✨
deconvR/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:deconvR-1.11.0(bioc 3.20)deconvR-1.10.0(bioc 3.19)

dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics

5.75 score 10 stars 14 scripts 264 downloads 4 exports 173 dependencies

Last updated 23 days agofrom:02212ba8f1. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 31 2024

Exports:BSmeth2ProbedeconvolutefindSignaturessimulateCellMix

Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64bbmlebdsmatrixbeanplotBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbumphuntercachemclassclicliprcodacodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdemingDerivdigestdoRNGdplyre1071emdbookfansifarverfastmapfastsegforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtablegtoolsHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmcrmemoisemethylKitmgcvmimeminfiminqamulttestmunsellmvtnormnlmenloptrnnlsnor1mixnumDerivopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogressproxypurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsrobslopesRsamtoolsrsqRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryamlzlibbioc

deconvR : Simulation and Deconvolution of Omic Profiles

Irem B. Gunduz, Veronika Ebenal, Altuna Akalin

Rendered fromdeconvRVignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

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