Showing 4 of total 4 results (show query)
bioc
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.
Maintained by Irem B. Gündüz. Last updated 5 months ago.
dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics
10 stars 5.78 score 15 scriptsbioc
granulator:Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data
granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.
Maintained by Sabina Pfister. Last updated 5 months ago.
rnaseqgeneexpressiondifferentialexpressiontranscriptomicssinglecellstatisticalmethodregression
3 stars 4.48 score 7 scripts
computationalproteomics
proteoDeconv:Enabling Cell-Type Deconvolution of Proteomics Data
Tools for deconvoluting proteomics data to identify and quantify cell types (e.g., immune cell types) in complex biological samples.
Maintained by Måns Zamore. Last updated 19 days ago.
2 stars 3.85 score
spang-lab
metabodecon:Deconvolution and Alignment of 1d NMR Spectra
A framework for deconvolution, alignment and postprocessing of 1-dimensional (1d) nuclear magnetic resonance (NMR) spectra, resulting in a data matrix of aligned signal integrals. The deconvolution part uses the algorithm described in Koh et al. (2009) <doi:10.1016/j.jmr.2009.09.003>. The alignment part is based on functions from the 'speaq' package, described in Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018> and Vu et al. (2011) <doi:10.1186/1471-2105-12-405>. A detailed description and evaluation of an early version of the package, 'MetaboDecon1D v0.2.2', can be found in Haeckl et al. (2021) <doi:10.3390/metabo11070452>.
Maintained by Tobias Schmidt. Last updated 7 days ago.
2 stars 3.70 score 2 scripts