- 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/3.20/data/experiment/html/RNAseqData.HNRNPC.bam.chr14.html
- License:
LGPL
- Recipe:
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¶
- Versions:
0.48.0-0,0.44.0-0,0.40.0-0,0.38.0-0,0.35.0-0,0.32.0-1,0.32.0-0,0.30.0-0,0.28.0-1,0.48.0-0,0.44.0-0,0.40.0-0,0.38.0-0,0.35.0-0,0.32.0-1,0.32.0-0,0.30.0-0,0.28.0-1,0.28.0-0,0.27.0-0,0.26.0-0,0.24.0-0,0.22.0-1,0.22.0-0,0.20.0-1,0.20.0-0- Depends:
on bioconductor-data-packages
>=20260207on curl
on r-base
>=4.5,<4.6.0a0
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-rnaseqdata.hnrnpc.bam.chr14
to add into an existing workspace instead, run:
pixi add bioconductor-rnaseqdata.hnrnpc.bam.chr14
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-rnaseqdata.hnrnpc.bam.chr14
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-rnaseqdata.hnrnpc.bam.chr14
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-rnaseqdata.hnrnpc.bam.chr14:<tag>
(see bioconductor-rnaseqdata.hnrnpc.bam.chr14/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/README.html)
