deco
This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see deco.
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Bioconductor version: 3.13
This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA. DECO reveals feature associations to hidden subclasses not exclusively related to higher deregulation levels.
Author: Francisco Jose Campos-Laborie, Jose Manuel Sanchez-Santos and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.
Maintainer: Francisco Jose Campos Laborie <fjcamlab at gmail.com>
citation("deco")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("deco")
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("deco")| deco | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, BiomedicalInformatics, Clustering, DifferentialExpression, ExonArray, FeatureExtraction, GeneExpression, MicroRNAArray, Microarray, MultipleComparison, Proteomics, RNASeq, Sequencing, Software, Transcription, Transcriptomics, mRNAMicroarray |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | GPL (>=3) |
| Depends | R (>= 3.5.0), AnnotationDbi, BiocParallel, SummarizedExperiment, limma |
| Imports | stats, methods, ggplot2, foreign, graphics, BiocStyle, Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4, sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2, gridExtra |
| System Requirements | |
| URL | https://github.com/fjcamlab/deco |
See More
| Suggests | knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens |
| 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 | deco_1.8.0.tar.gz |
| Windows Binary | deco_1.8.0.zip |
| macOS 10.13 (High Sierra) | deco_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/deco |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/deco |
| Bioc Package Browser | https://code.bioconductor.org/browse/deco/ |
| Package Short Url | https://bioconductor.org/packages/deco/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |