To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ind1KG")
In most cases, you don't need to download the package archive at all.
ind1KG
Data from 1000 Genomes, NA19240 (female) chr6 excerpt
Bioconductor version: 3.0
Elements of samtools/bioc workflow for dealing with personal sequence focusing on identification and interpretation of rare variants
Author: VJ Carey <stvjc at channing.harvard.edu>
Maintainer: VJ Carey <stvjc at channing.harvard.edu>
Citation (from within R,
enter citation("ind1KG")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ind1KG")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ind1KG")
| R Script | ind1KG -- 1000 genomes data demo | |
| R Script | Notes for eSet developers | |
| Reference Manual |
Details
| biocViews | ExperimentData, Genetics, HighThroughputSequencing |
| Version | 0.3.1 |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.1), chopsticks |
| Imports | |
| LinkingTo | |
| Suggests | Rsamtools, rtracklayer, GenomicFeatures, org.Hs.eg.db, SNPlocs.Hsapiens.dbSNP.20090506, TxDb.Hsapiens.UCSC.hg18.knownGene, lumiHumanIDMapping, GGBase, GGtools, hmyriB36 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ind1KG_0.3.1.tar.gz |
| Windows Binary | ind1KG_0.3.1.zip |
| Mac OS X 10.6 (Snow Leopard) | ind1KG_0.3.1.tgz |
| Mac OS X 10.9 (Mavericks) | ind1KG_0.3.1.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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