recipe bioconductor-seqsqc

The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/SeqSQC.html

License

GPL-3

Recipe

/bioconductor-seqsqc/meta.yaml

package bioconductor-seqsqc

(downloads) docker_bioconductor-seqsqc

Versions

1.4.0-0

Depends bioconductor-experimenthub

>=1.8.0,<1.9.0

Depends bioconductor-gdsfmt

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-snprelate

>=1.16.0,<1.17.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-e1071

Depends r-ggally

Depends r-ggplot2

Depends r-rbokeh

Depends r-rcolorbrewer

Depends r-reshape2

Depends r-rmarkdown

Requirements

Installation

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

conda install bioconductor-seqsqc

and update with:

conda update bioconductor-seqsqc

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-seqsqc:<tag>

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