recipe bioconductor-codex

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

Homepage:

https://bioconductor.org/packages/3.20/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

(downloads) docker_bioconductor-codex

Versions:
1.42.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0, 

1.42.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  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:

  • on bioconductor-biostrings >=2.78.0,<2.79.0

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

  • on bioconductor-genomeinfodb >=1.46.0,<1.47.0

  • on bioconductor-iranges >=2.44.0,<2.45.0

  • on bioconductor-rsamtools >=2.26.0,<2.27.0

  • on bioconductor-s4vectors >=0.48.0,<0.49.0

  • on r-base >=4.5,<4.6.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-codex

to add into an existing workspace instead, run:

pixi add bioconductor-codex

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-codex

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-codex

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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