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biocLite("chopsticks")
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chopsticks
The snp.matrix and X.snp.matrix classes
Bioconductor version: 3.0
Implements classes and methods for large-scale SNP association studies
Author: Hin-Tak Leung <htl10 at users.sourceforge.net>
Maintainer: Hin-Tak Leung <htl10 at users.sourceforge.net>
Citation (from within R,
enter citation("chopsticks")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("chopsticks")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("chopsticks")
| R Script | snpMatrix | |
| Reference Manual |
Details
| biocViews | GeneticVariability, Microarray, SNP, SNPsAndGeneticVariability, Software |
| Version | 1.30.1 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| License | GPL-3 |
| Depends | R (>= 2.10.0), survival, methods |
| Imports | |
| LinkingTo | |
| Suggests | hexbin |
| SystemRequirements | |
| Enhances | |
| URL | http://outmodedbonsai.sourceforge.net/ |
| Depends On Me | ind1KG |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | chopsticks_1.30.1.tar.gz |
| Windows Binary | chopsticks_1.30.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | chopsticks_1.30.1.tgz |
| Mac OS X 10.9 (Mavericks) | chopsticks_1.30.1.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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