recipe bioconductor-ddct

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

Homepage:

https://bioconductor.org/packages/3.18/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:
1.62.0-0,  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, 

1.62.0-0,  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 bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends r-base:

>=4.4,<4.5.0a0

depends r-lattice:

depends r-rcolorbrewer:

>=0.1-3

depends r-xtable:

requirements:

additional platforms:

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-ddct

and update with::

   mamba update bioconductor-ddct

To create a new environment, run:

mamba create --name myenvname bioconductor-ddct

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-ddct:<tag>

(see `bioconductor-ddct/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ddct/README.html)