Package: deconvR 1.19.0

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_1.19.0.tar.gz
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deconvR_1.19.0.tgz(r-4.6-any)deconvR_1.19.0.tgz(r-4.5-any)
deconvR_1.19.0.tar.gz(r-4.7-any)deconvR_1.19.0.tar.gz(r-4.6-any)
deconvR_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
deconvR/json (API)

# Install 'deconvR' in R:

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

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

Datasets:

HumanCellTypeMethAtlas - The comprehensive human methylome reference atlas
IlluminaMethEpicB5ProbeIDs - A dataset Illumina probe IDs of 400000 genomic loci (identified using the “seqnames”, “ranges”, and “strand” values).

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

dnamethylation regression geneexpression rnaseq singlecell statisticalmethod transcriptomics bioconductor-package deconvolution dna-methylation omics

6.12 score 10 stars 22 scripts 4 exports 178 dependencies

Last updated from:2779e925bb. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	266
linux-devel-x86_64	OK	879
source / vignettes	OK	362
linux-release-x86_64	OK	926
macos-release-arm64	OK	702
macos-oldrel-arm64	OK	455
windows-devel	OK	740
windows-release	OK	774
windows-oldrel	OK	723
wasm-release	OK	242

Exports:BSmeth2Probe deconvolute findSignatures simulateCellMix

Dependencies:abind annotate AnnotationDbi askpass assertthat base64 bbmle bdsmatrix beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob boot bumphunter cachem cigarillo class cli clipr coda codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deming Deriv digest dir.expiry doRNG dplyr e1071 emdbook farver fastmap fastseg filelock foreach formatR futile.logger futile.options genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable gtools h5mread HDF5Array hms httr httr2 illuminaio IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma lme4 locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust mcr memoise methylKit mgcv mime minfi minqa multtest mvtnorm nlme nloptr nnls nor1mix numDeriv openssl pillar pkgconfig plyr png preprocessCore prettyunits progress proxy purrr quadprog qvalue R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr reformulas rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools robslopes Rsamtools rsq RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml

deconvR : Simulation and Deconvolution of Omic Profiles

Rendered fromdeconvRVignette.Rmdusingknitr::rmarkdown

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

Help page	Topics
A function to map WGBS methylation data to Illumina Probe IDs	BSmeth2Probe
A function to deconvolute of bulk samples to their origin proportions using data from reference atlas (e.g. methylation signatures) Results of model are returned in dataframe "results". Summary of partial R-squared values of model (min, median, mean, max) are printed upon completion.	deconvolute
A function to construct a signature matrix	findSignatures
The comprehensive human methylome reference atlas	HumanCellTypeMethAtlas
A dataset Illumina probe IDs of 400000 genomic loci (identified using the “seqnames”, “ranges”, and “strand” values).	IlluminaMethEpicB5ProbeIDs
A function to generate a dataframe of mixed cell-type origin simulated samples using given reference atlas.	simulateCellMix

Package: deconvR 1.19.0

deconvR: Simulation and Deconvolution of Omic Profiles

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