To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("seqCNA")
In most cases, you don't need to download the package archive at all.
seqCNA
Copy number analysis of high-throughput sequencing cancer data
Bioconductor version: 3.0
Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization
Author: David Mosen-Ansorena
Maintainer: David Mosen-Ansorena <dmosen.gn at cicbiogune.es>
Citation (from within R,
enter citation("seqCNA")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("seqCNA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("seqCNA")
| R Script | seqCNA | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Genetics, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-3 |
| Depends | R (>= 3.0), GLAD(>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot(>= 0.99), methods |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | samtools |
| Enhances | |
| 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 | seqCNA_1.10.0.tar.gz |
| Windows Binary | seqCNA_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | seqCNA_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | seqCNA_1.10.0.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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