recipe bioconductor-qdnaseq

Quantitative DNA Sequencing for Chromosomal Aberrations

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/QDNAseq.html

License:

GPL

Recipe:

/bioconductor-qdnaseq/meta.yaml

Links:

biotools: qdnaseq

Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

package bioconductor-qdnaseq

Versions:

1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.0-0, 

1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-cghbase >=1.58.0,<1.59.0

• bioconductor-cghcall >=2.60.0,<2.61.0

• bioconductor-dnacopy >=1.72.0,<1.73.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• r-base >=4.2,<4.3.0a0

• r-future.apply >=1.8.1

• r-matrixstats >=0.60.0

• r-r.utils >=2.9.0

Required By:

• bioconductor-hiccompare

• bioconductor-qdnaseq.hg19

• bioconductor-ace

• bioconductor-biscuiteer

• bioconductor-qdnaseq.mm10

• bioconductor-genebreak

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-qdnaseq

and update with:

conda update bioconductor-qdnaseq

or use the docker container:

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

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-qdnaseq/README.html)