debCAM

DOI: 10.18129/B9.bioc.debCAM    

Deconvolution by Convex Analysis of Mixtures

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script debCAM User Manual
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBiology, GeneExpression, Software
Version 1.4.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License GPL-2
Depends R (>= 3.5)
Imports methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
SystemRequirements Java (>= 1.8)
Enhances
URL
BugReports https://github.com/Lululuella/debCAM/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package debCAM_1.4.0.tar.gz
Windows Binary debCAM_1.4.0.zip
Mac OS X 10.11 (El Capitan) debCAM_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/debCAM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/debCAM
Package Short Url https://bioconductor.org/packages/debCAM/
Package Downloads Report Download Stats

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