recipe bioconductor-seqcat

High Throughput Sequencing Cell Authentication Toolkit

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/seqCAT.html

License:

MIT + file LICENCE

Recipe:

/bioconductor-seqcat/meta.yaml

The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.

package bioconductor-seqcat

versions:

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.1-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0, 

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.1-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.3-0,  1.6.0-1,  1.4.1-0,  1.4.0-0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-variantannotation:

>=1.52.0,<1.53.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

>=0.5.0

depends r-ggplot2:

>=2.2.1

depends r-rlang:

depends r-scales:

>=0.4.1

depends r-tidyr:

>=0.6.1

requirements:

additional platforms:

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-seqcat

and update with::

   mamba update bioconductor-seqcat

To create a new environment, run:

mamba create --name myenvname bioconductor-seqcat

with myenvname being 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-seqcat:<tag>

(see `bioconductor-seqcat/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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