recipe bioconductor-htsfilter

Filter replicated high-throughput transcriptome sequencing data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/HTSFilter.html

License:

Artistic-2.0

Recipe:

/bioconductor-htsfilter/meta.yaml

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

package bioconductor-htsfilter

(downloads) docker_bioconductor-htsfilter

versions:
1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.1-0,  1.22.0-0, 

1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.1-0,  1.22.0-0,  1.20.0-0,  1.18.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-deseq2:

>=1.40.0,<1.41.0

depends bioconductor-edger:

>=3.42.0,<3.43.0

depends r-base:

>=4.3,<4.4.0a0

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-htsfilter

and update with::

   mamba update bioconductor-htsfilter

To create a new environment, run:

mamba create --name myenvname bioconductor-htsfilter

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-htsfilter:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-htsfilter/README.html)