CAMTHC

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CAMTHC (renamed to debCAM).

Convex Analysis of Mixtures for Tissue Heterogeneity Characterization


Bioconductor version: 3.9

An R package for tissue heterogeneity characterization by convex analysis of mixtures (CAM). It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by 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("CAMTHC")):

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("CAMTHC")

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

Details

biocViews CellBiology, GeneExpression, Software
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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/CAMTHC/issues
See More
Suggests knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
Linking To
Enhances
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Imports Me
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Build Report Build Report

Package Archives

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

Source Package CAMTHC_1.2.0.tar.gz
Windows Binary CAMTHC_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CAMTHC_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CAMTHC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CAMTHC
Bioc Package Browser https://code.bioconductor.org/browse/CAMTHC/
Package Short Url https://bioconductor.org/packages/CAMTHC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive