- recipe bioconductor-cnvpanelizer
Reliable CNV detection in targeted sequencing applications
- Homepage:
https://bioconductor.org/packages/3.14/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:
1.26.0-0
,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
,1.8.0-0
- Depends:
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-exomecopy
>=1.40.0,<1.41.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-noiseq
>=2.38.0,<2.39.0
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-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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-cnvpanelizer/README.html)