recipe bioconductor-seqc

RNA-seq data generated from SEQC (MAQC-III) study

Homepage:

https://bioconductor.org/packages/3.20/data/experiment/html/seqc.html

License:

GPL-3

Recipe:

/bioconductor-seqc/meta.yaml

The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well.

package bioconductor-seqc

(downloads) docker_bioconductor-seqc

Versions:
1.44.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1, 

1.44.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0

Depends:

  • on bioconductor-biobase >=2.70.0,<2.71.0

  • on bioconductor-data-packages >=20260207

  • on 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-seqc

to add into an existing workspace instead, run:

pixi add bioconductor-seqc

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-seqc

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-seqc

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-seqc:<tag>

(see bioconductor-seqc/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.

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