recipe bioconductor-rnaseqdata.hnrnpc.bam.chr14

Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/RNAseqData.HNRNPC.bam.chr14.html

License:

LGPL

Recipe:

/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml

The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files.

package bioconductor-rnaseqdata.hnrnpc.bam.chr14

(downloads) docker_bioconductor-rnaseqdata.hnrnpc.bam.chr14

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,  0.20.0-1,  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-rnaseqdata.hnrnpc.bam.chr14

and update with::

   mamba update bioconductor-rnaseqdata.hnrnpc.bam.chr14

To create a new environment, run:

mamba create --name myenvname bioconductor-rnaseqdata.hnrnpc.bam.chr14

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-rnaseqdata.hnrnpc.bam.chr14:<tag>

(see `bioconductor-rnaseqdata.hnrnpc.bam.chr14/tags`_ for valid values for ``<tag>``)

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