recipe bioconductor-doqtl

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.







biotools: doqtl

package bioconductor-doqtl

(downloads) docker_bioconductor-doqtl


1.18.0-0, 1.16.2-0, 1.14.0-0

Depends bioconductor-annotate


Depends bioconductor-annotationtools


Depends bioconductor-biobase


Depends bioconductor-biocgenerics


Depends bioconductor-biomart


Depends bioconductor-bsgenome.mmusculus.ucsc.mm10


Depends bioconductor-genomicranges


Depends bioconductor-iranges


Depends bioconductor-rhdf5


Depends bioconductor-rsamtools


Depends bioconductor-variantannotation


Depends libgcc-ng


Depends r-base


Depends r-corpcor

Depends r-doparallel

Depends r-foreach

Depends r-fpc

Depends r-hwriter

Depends r-iterators

Depends r-mclust

Depends r-qtlrel

Depends r-regress

Depends r-runit

Depends r-xml



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-doqtl

and update with:

conda update bioconductor-doqtl

or use the docker container:

docker pull<tag>

(see bioconductor-doqtl/tags for valid values for <tag>)