recipe cnvkit

Copy number variant detection from high-throughput sequencing

Homepage:

https://github.com/etal/cnvkit

License:

Apache-2.0

Recipe:

/cnvkit/meta.yaml

Links:

biotools: cnvkit, doi: 10.1371/journal.pcbi.1004873

package cnvkit

Versions:

0.9.10-0,  0.9.9-0,  0.9.8-0,  0.9.7-1,  0.9.7-0,  0.9.6-2,  0.9.6-1,  0.9.6-0,  0.9.6a0-2, 

0.9.10-0,  0.9.9-0,  0.9.8-0,  0.9.7-1,  0.9.7-0,  0.9.6-2,  0.9.6-1,  0.9.6-0,  0.9.6a0-2,  0.9.6a0-1,  0.9.6a0-0,  0.9.5-1,  0.9.5-0,  0.9.4a0-0,  0.9.3-2,  0.9.2-2,  0.9.2a0-2,  0.9.2a0-1,  0.9.2a0-0,  0.9.1-0,  0.9.1a0-0,  0.9.0-0,  0.8.6a0-2,  0.8.6a0-1,  0.8.6a0-0,  0.8.5-0,  0.8.5dev0-1,  0.8.5dev0-0,  0.8.4-0,  0.8.3a0-1,  0.8.3a0-0,  0.8.2-0,  0.8.1-0,  0.8.0-0,  0.7.11-0,  0.7.10-1,  0.7.10-0,  0.7.9-0,  0.7.8-1,  0.7.8-0,  0.7.7-0,  0.7.6-0,  0.7.5-0,  0.7.4-1,  0.7.4-0,  0.7.3-0

Depends:

• bioconductor-dnacopy

• biopython >=1.62

• joblib <1.0

• matplotlib-base >=1.3.1

• networkx >=2.4

• numpy >=1.9

• pandas >=0.23.3

• pomegranate >=0.9.0

• pyfaidx >=0.4.7

• pysam >=0.16.0

• python >=3.5

• r-base >=3.4.1

• r-cghflasso

• reportlab >=3.0

• scipy >=0.15.0

Required By:

• hmnqc

Installation

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

conda install cnvkit

and update with:

conda update cnvkit

or use the docker container:

docker pull quay.io/biocontainers/cnvkit:<tag>

(see cnvkit/tags for valid values for <tag>)

Download stats

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