recipe bioconductor-teqc

Quality control for target capture experiments

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TEQC.html

License:

GPL (>= 2)

Recipe:

/bioconductor-teqc/meta.yaml

Links:

biotools: teqc, doi: 10.1093/bioinformatics/btr122

Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

package bioconductor-teqc

versions:

4.24.0-0,  4.22.0-0,  4.20.0-0,  4.16.0-0,  4.14.0-0,  4.12.0-1,  4.12.0-0,  4.10.0-0,  4.8.0-0, 

4.24.0-0,  4.22.0-0,  4.20.0-0,  4.16.0-0,  4.14.0-0,  4.12.0-1,  4.12.0-0,  4.10.0-0,  4.8.0-0,  4.6.0-1,  4.4.0-0,  4.2.0-0,  3.18.0-0,  3.16.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-hwriter:

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-teqc

and update with::

   mamba update bioconductor-teqc

To create a new environment, run:

mamba create --name myenvname bioconductor-teqc

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-teqc:<tag>

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

Download stats

Link to this page

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