Package: DOQTL
Version: 1.8.0
Date: 2012-12-07
Title: Genotyping and QTL Mapping in DO Mice
Author: Daniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek
Maintainer: Daniel Gatti <Dan.Gatti@jax.org>
Depends: R (>= 3.0.0), BSgenome.Mmusculus.UCSC.mm10, GenomicRanges, VariantAnnotation
Imports: annotate, annotationTools, biomaRt, Biobase, BiocGenerics, corpcor, doParallel, foreach, fpc, hwriter, IRanges, iterators, mclust, QTLRel, regress, rhdf5, Rsamtools, RUnit, XML
Suggests: MUGAExampleData, doMPI
Description: 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.
biocViews: GeneticVariability, SNP, Genetics, HiddenMarkovModel
License: GPL-3
LazyData: true
ByteCompile: yes
URL: http://do.jax.org
NeedsCompilation: yes
Packaged: 2016-05-04 05:39:30 UTC; biocbuild
Package: BSgenome.Mmusculus.UCSC.mm10.masked
Title: Full masked genome sequences for Mus musculus (UCSC version
mm10)
Description: Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, Dec. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm10, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask).
Version: 1.3.99
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
Depends: BSgenome (>= 1.31.8), BSgenome.Mmusculus.UCSC.mm10
Imports: BSgenome, BSgenome.Mmusculus.UCSC.mm10
License: Artistic-2.0
organism: Mus musculus
species: Mouse
provider: UCSC
provider_version: mm10
release_date: Dec. 2011
release_name: Genome Reference Consortium GRCm38
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/
biocViews: AnnotationData, Genetics, BSgenome, Mus_musculus
Packaged: 2014-01-08 20:13:56 UTC; hpages
providing 
.