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biocLite("SeqArray")
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SeqArray
Big Data Management of Genome-wide Sequencing Variants
Bioconductor version: 3.0
Big data management of genome-wide variants using the CoreArray C++ library: genotypic data and annotations are stored in an array-oriented manner, offering efficient access of genetic variants using the S programming language.
Author: Xiuwen Zheng [aut, cre], Stephanie Gogarten [aut], Cathy Laurie [ctb]
Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>
Citation (from within R,
enter citation("SeqArray")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SeqArray")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SeqArray")
| R Script | SeqArray | |
| SeqArray-JSM2013.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Genetics, Infrastructure, Sequencing, Software |
| Version | 1.6.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | GPL-3 |
| Depends | gdsfmt(>= 1.1.0) |
| Imports | methods, Biostrings, GenomicRanges, IRanges, S4Vectors, VariantAnnotation |
| LinkingTo | gdsfmt |
| Suggests | parallel, BiocStyle, BiocGenerics, RUnit, Rcpp |
| SystemRequirements | |
| Enhances | |
| URL | http://corearray.sourceforge.net/tutorials/SeqArray/ http://github.com/zhengxwen/SeqArray |
| Depends On Me | SeqVarTools |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SeqArray_1.6.1.tar.gz |
| Windows Binary | SeqArray_1.6.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | SeqArray_1.6.1.tgz |
| Mac OS X 10.9 (Mavericks) | SeqArray_1.6.1.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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