To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GGBase")
In most cases, you don't need to download the package archive at all.
GGBase
GGBase infrastructure for genetics of gene expression package GGtools
Bioconductor version: 3.0
infrastructure
Author: VJ Carey <stvjc at channing.harvard.edu>
Maintainer: VJ Carey <stvjc at channing.harvard.edu>
Citation (from within R,
enter citation("GGBase")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GGBase")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GGBase")
| R Script | GGBase -- infrastructure for GGtools, genetics of gene expression | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Genetics, Infrastructure, Software |
| Version | 3.28.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14), methods, snpStats |
| Imports | limma, genefilter, Biobase, BiocGenerics, Matrix, AnnotationDbi, digest, GenomicRanges |
| LinkingTo | |
| Suggests | GGtools, illuminaHumanv1.db |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | ceu1kg, ceu1kgv, ceuhm3, dsQTL, encoDnaseI, GGdata, GGtools, hmyriB36, yri1kgv |
| Imports Me | |
| Suggests Me | ind1KG |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GGBase_3.28.0.tar.gz |
| Windows Binary | GGBase_3.28.0.zip |
| Mac OS X 10.6 (Snow Leopard) | GGBase_3.28.0.tgz |
| Mac OS X 10.9 (Mavericks) | GGBase_3.28.0.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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