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biocLite("ADaCGH2")
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ADaCGH2
Analysis of big data from aCGH experiments using parallel computing and ff objects
Bioconductor version: 3.0
Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Author: Ramon Diaz-Uriarte <rdiaz02 at gmail.com> and Oscar M. Rueda <rueda.om at gmail.com>. Wavelet-based aCGH smoothing code from Li Hsu <lih at fhcrc.org> and Douglas Grove <dgrove at fhcrc.org>. Imagemap code from Barry Rowlingson <B.Rowlingson at lancaster.ac.uk>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>.
Maintainer: Ramon Diaz-Uriarte <rdiaz02 at gmail.com>
Citation (from within R,
enter citation("ADaCGH2")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ADaCGH2")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ADaCGH2")
| R Script | ADaCGH2 Overview | |
| ADaCGH2-long-examples.pdf | ||
| benchmarks.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariants, Microarray, Software |
| Version | 2.6.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) |
| License | GPL (>= 3) |
| Depends | R (>= 2.15.0), parallel, ff |
| Imports | bit, ffbase, DNAcopy, tilingArray, GLAD, waveslim, cluster, aCGH, snapCGH |
| LinkingTo | |
| Suggests | CGHregions, Cairo, limma |
| SystemRequirements | |
| Enhances | Rmpi |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ADaCGH2_2.6.0.tar.gz |
| Windows Binary | ADaCGH2_2.6.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ADaCGH2_2.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | ADaCGH2_2.6.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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