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source("http://bioconductor.org/biocLite.R")
biocLite("gwascat")
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gwascat
representing and modeling data in the NHGRI GWAS catalog
Bioconductor version: 3.0
representing and modeling data in the NHGRI GWAS catalog
Author: VJ Carey <stvjc at channing.harvard.edu>
Maintainer: VJ Carey <stvjc at channing.harvard.edu>
Citation (from within R,
enter citation("gwascat")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("gwascat")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gwascat")
| R Script | gwascat -- exploring NHGRI GWAS catalog | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Genetics, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0) |
| Imports | methods, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, snpStats, Biostrings, Rsamtools, rtracklayer |
| LinkingTo | |
| Suggests | DO.db, Gviz, ggbio, graph |
| SystemRequirements | |
| Enhances | SNPlocs.Hsapiens.dbSNP.20120608, pd.genomewidesnp.6 |
| URL | |
| Depends On Me | vtpnet |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | gwascat_1.10.0.tar.gz |
| Windows Binary | gwascat_1.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | gwascat_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | gwascat_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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