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debCAM

Deconvolution by Convex Analysis of Mixtures


Bioconductor version: Release (3.18)

An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.

Author: Lulu Chen <luluchen at vt.edu>

Maintainer: Lulu Chen <luluchen at vt.edu>

Citation (from within R, enter citation("debCAM")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("debCAM")

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("debCAM")
debCAM User Manual HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBiology, GeneExpression, Software
Version 1.20.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-2
Depends R (>= 3.5)
Imports methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics
System Requirements Java (>= 1.8)
URL
Bug Reports https://github.com/Lululuella/debCAM/issues
See More
Suggests knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
Linking To
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Build Report Build Report

Package Archives

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

Source Package debCAM_1.20.0.tar.gz
Windows Binary debCAM_1.20.0.zip
macOS Binary (x86_64) debCAM_1.20.0.tgz
macOS Binary (arm64) debCAM_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/debCAM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/debCAM
Bioc Package Browser https://code.bioconductor.org/browse/debCAM/
Package Short Url https://bioconductor.org/packages/debCAM/
Package Downloads Report Download Stats