recipe bioconductor-countsimqc

Compare Characteristic Features of Count Data Sets

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-countsimqc/meta.yaml

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

package bioconductor-countsimqc

versions:

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.1-0,  1.8.0-0,  1.6.0-0,  1.4.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.1-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-genomeinfodbdata:

>=1.2.0,<1.3.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-catools:

depends r-dplyr:

depends r-dt:

depends r-ggplot2:

depends r-ragg:

depends r-randtests:

depends r-rmarkdown:

>=2.5

depends r-tidyr:

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-countsimqc

and update with::

   mamba update bioconductor-countsimqc

To create a new environment, run:

mamba create --name myenvname bioconductor-countsimqc

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-countsimqc:<tag>

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

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