recipe bioconductor-codex

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Homepage

https://bioconductor.org/packages/3.11/bioc/html/CODEX.html

License

GPL-2

Recipe

/bioconductor-codex/meta.yaml

Links

biotools: codex, doi: 10.1093/nar/gku1363

A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.

package bioconductor-codex

Versions

1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0

Depends

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

Required By

• bioconductor-icnv

Installation

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

conda install bioconductor-codex

and update with:

conda update bioconductor-codex

or use the docker container:

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

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

Link to this page

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