recipe bioconductor-ddct

The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/ddCt.html

License:

LGPL-3

Recipe:

/bioconductor-ddct/meta.yaml

Links:

biotools: ddct, doi: 10.1038/nmeth.3252

The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

package bioconductor-ddct

(downloads) docker_bioconductor-ddct

Versions:
1.66.0-0,  1.62.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0, 

1.66.0-0,  1.62.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0,  1.44.0-0,  1.42.0-0,  1.40.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-0

Depends:

  • on bioconductor-biobase >=2.70.0,<2.71.0

  • on bioconductor-biocgenerics >=0.56.0,<0.57.0

  • on r-base >=4.5,<4.6.0a0

  • on r-lattice

  • on r-rcolorbrewer >=0.1-3

  • on r-xtable

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-ddct

to add into an existing workspace instead, run:

pixi add bioconductor-ddct

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-ddct

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ddct

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-ddct:<tag>

(see bioconductor-ddct/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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