recipe bioconductor-pasillabamsubset

Subset of BAM files from "Pasilla" experiment

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/pasillaBamSubset.html

License:

LGPL

Recipe:

/bioconductor-pasillabamsubset/meta.yaml

Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped.

package bioconductor-pasillabamsubset

(downloads) docker_bioconductor-pasillabamsubset

versions:
0.40.0-0,  0.38.0-0,  0.35.0-0,  0.32.0-1,  0.32.0-0,  0.30.0-0,  0.28.0-1,  0.28.0-0,  0.27.0-0, 

0.40.0-0,  0.38.0-0,  0.35.0-0,  0.32.0-1,  0.32.0-0,  0.30.0-0,  0.28.0-1,  0.28.0-0,  0.27.0-0,  0.26.0-0,  0.24.0-0,  0.22.0-1,  0.22.0-0,  0.20.0-0

depends bioconductor-data-packages:

>=20231203

depends curl:

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-pasillabamsubset

and update with::

   mamba update bioconductor-pasillabamsubset

To create a new environment, run:

mamba create --name myenvname bioconductor-pasillabamsubset

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-pasillabamsubset:<tag>

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

Download stats

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-pasillabamsubset/README.html)