-
recipe
bioconductor-cnvpanelizer
Reliable CNV detection in targeted sequencing applications
- Homepage
https://bioconductor.org/packages/3.12/bioc/html/CNVPanelizer.html
- License
GPL-3
- Recipe
- Links
biotools: cnvpanelizer, doi: 10.1038/nmeth.3252
A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.
-
package
bioconductor-cnvpanelizer
¶ -
- Versions
1.22.0-0
,1.20.0-0
,1.18.0-0
,1.16.0-1
,1.14.0-0
,1.12.0-0
,1.8.0-0
- Depends
bioconductor-biocgenerics
>=0.36.0,<0.37.0
bioconductor-exomecopy
>=1.36.0,<1.37.0
bioconductor-genomeinfodb
>=1.26.0,<1.27.0
bioconductor-genomicranges
>=1.42.0,<1.43.0
bioconductor-iranges
>=2.24.0,<2.25.0
bioconductor-noiseq
>=2.34.0,<2.35.0
bioconductor-rsamtools
>=2.6.0,<2.7.0
bioconductor-s4vectors
>=0.28.0,<0.29.0
r-base
>=4.0,<4.1.0a0
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-cnvpanelizer
and update with:
conda update bioconductor-cnvpanelizer
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-cnvpanelizer:<tag>
(see bioconductor-cnvpanelizer/tags for valid values for
<tag>
)
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-cnvpanelizer/README.html)