Package: deconvR 1.11.0

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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NEWS

# 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-1.11.0(bioc 3.20)deconvR-1.10.0(bioc 3.19)

bioconductor-package

4 exports 0.71 score 165 dependencies

Last updated 2 months agofrom:1de875b21d

Exports:BSmeth2Probe deconvolute findSignatures simulateCellMix

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

deconvR : Simulation and Deconvolution of Omic Profiles

Irem B. Gunduz, Veronika Ebenal, Altuna Akalin

Rendered fromdeconvRVignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

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 1.11.0

deconvR: Simulation and Deconvolution of Omic Profiles

deconvR : Simulation and Deconvolution of Omic Profiles

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