- recipe bioconductor-podkat
Position-Dependent Kernel Association Test
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/podkat.html
- License:
GPL (>= 2)
- Recipe:
- Links:
biotools: podkat, doi: 10.1038/nmeth.3252
This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.
- package bioconductor-podkat¶
- versions:
1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.26.0-2,1.26.0-1,1.26.0-0,1.24.0-0,1.22.0-1,1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.26.0-2,1.26.0-1,1.26.0-0,1.24.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-0,1.16.0-1,1.14.0-1,1.14.0-0,1.12.0-0,1.10.0-0,1.8.0-0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-matrix:
- depends r-rcpp:
>=0.11.1- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-podkat and update with:: mamba update bioconductor-podkat
To create a new environment, run:
mamba create --name myenvname bioconductor-podkat
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-podkat:<tag> (see `bioconductor-podkat/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-podkat/README.html)
