To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DOQTL")
In most cases, you don't need to download the package archive at all.
DOQTL
Genotyping and QTL Mapping in DO Mice
Bioconductor version: 3.0
DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.
Author: Daniel Gatti, Karl Broman, Andrey Shabalin
Maintainer: Daniel Gatti <Dan.Gatti at jax.org>
Citation (from within R,
enter citation("DOQTL")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DOQTL")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DOQTL")
| R Script | QTL Mapping using Diversity Outbred Mice | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneticVariability, Genetics, HiddenMarkovModel, SNP, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 2.10.0) |
| Imports | annotate, annotationTools, biomaRt, Biobase, BiocGenerics, corpcor, GenomicRanges, hwriter, IRanges, mclust, MUGAExampleData, org.Hs.eg.db, org.Mm.eg.db, QTLRel, Rsamtools, RUnit, XML |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://do.jax.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DOQTL_1.0.0.tar.gz |
| Windows Binary | DOQTL_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DOQTL_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | DOQTL_1.0.0.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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