- recipe bioconductor-codex
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
- Homepage:
- License:
GPL-2
- Recipe:
- 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:
1.26.0-0
,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
,1.26.0-0
,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:
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-bsgenome.hsapiens.ucsc.hg19
>=1.4.0,<1.5.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
r-base
>=4.1,<4.2.0a0
- Required By:
Installation
With an activated Bioconda channel (see 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-codex/README.html)