A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from https://www.bioconductor.org/packages/release/bioc/html/deconvR.html below:

Bioconductor - deconvR

deconvR

This is the released version of deconvR; for the devel version, see deconvR.

Simulation and Deconvolution of Omic Profiles

Bioconductor version: Release (3.21)

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.

Author: Irem B. Gündüz [aut, cre] ORCID: 0000-0003-2641-0916 , Veronika Ebenal [aut] ORCID: 0000-0001-7976-3964 , Altuna Akalin [aut] ORCID: 0000-0002-0468-0117

Maintainer: Irem B. Gündüz <irembgunduz at gmail.com>

Citation (from within R, enter citation("deconvR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("deconvR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("deconvR")
Details biocViews DNAMethylation, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics Version 1.14.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License Artistic-2.0 Depends R (>= 4.1), data.table (>= 1.14.0) Imports S4Vectors(>= 0.30.0), methylKit(>= 1.18.0), IRanges(>= 2.26.0), GenomicRanges(>= 1.44.0), BiocGenerics(>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi System Requirements URL https://github.com/BIMSBbioinfo/deconvR Bug Reports https://support.bioconductor.org/t/deconvR See More Suggests testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle(>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4