debCAM
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see debCAM.
Deconvolution by Convex Analysis of Mixtures
Bioconductor version: 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("debCAM")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | CellBiology, GeneExpression, Software |
| Version | 1.4.0 |
| 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, DMwR, 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 | |
| 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.
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/debCAM/ |
| Package Short Url | https://bioconductor.org/packages/debCAM/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |