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cheung2010
resources for genetics of gene expression based on Cheung et al 2010
Bioconductor version: 3.0
Data resources related to the PLoS Biology paper Polymorphic Cis- and Trans-Regulation of Human Gene Expression, including small-footprint smlSet support for 147 hgfocus arrays and corresponding HapMap genotypes at 1.3 million SNP; 0.0.22+ includes cheung_eset... from Leek et al RECOUNT myrna output
Author: Vince Carey <stvjc at channing.harvard.edu>
Maintainer: Vince Carey <stvjc at channing.harvard.edu>
Citation (from within R,
enter citation("cheung2010")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("cheung2010")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cheung2010")
| R Script | cheungTrans: checking trans eQTL with hgfocus arrays | |
| Reference Manual |
Details
| biocViews | ExperimentData, GeneticVariability, RNAseqData |
| Version | 0.3.2 |
| License | Artistic-2.0 |
| Depends | R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db |
| Imports | AnnotationDbi |
| LinkingTo | |
| Suggests | SNPlocs.Hsapiens.dbSNP.20120608 |
| SystemRequirements | |
| Enhances | parallel |
| URL | |
| Depends On Me | ggtut |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | cheung2010_0.3.2.tar.gz |
| Windows Binary | cheung2010_0.3.2.zip |
| Mac OS X 10.6 (Snow Leopard) | cheung2010_0.3.2.tgz |
| Mac OS X 10.9 (Mavericks) | cheung2010_0.3.2.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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