recipe bioconductor-hivcdnavantwout03

T cell line infections with HIV-1 LAI (BRU)

Homepage:

https://bioconductor.org/packages/3.20/data/experiment/html/HIVcDNAvantWout03.html

License:

GPL (>= 2)

Recipe:

/bioconductor-hivcdnavantwout03/meta.yaml

The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw).

package bioconductor-hivcdnavantwout03

(downloads) docker_bioconductor-hivcdnavantwout03

Versions:
1.50.0-0,  1.46.0-0,  1.42.0-0,  1.40.0-0,  1.37.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1, 

1.50.0-0,  1.46.0-0,  1.42.0-0,  1.40.0-0,  1.37.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.29.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0

Depends:

  • 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-hivcdnavantwout03

to add into an existing workspace instead, run:

pixi add bioconductor-hivcdnavantwout03

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-hivcdnavantwout03

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hivcdnavantwout03

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-hivcdnavantwout03:<tag>

(see bioconductor-hivcdnavantwout03/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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