recipe bioconductor-podcall

Positive Droplet Calling for DNA Methylation Droplet Digital PCR

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/PoDCall.html

License:

GPL-3

Recipe:

/bioconductor-podcall/meta.yaml

Reads files exported from 'QX Manager or QuantaSoft' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

package bioconductor-podcall

versions:

1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-diptest:

depends r-dt:

depends r-ggplot2:

depends r-gridextra:

depends r-laplacesdemon:

depends r-mclust:

depends r-purrr:

depends r-readr:

depends r-rlist:

depends r-shiny:

depends r-shinyjs:

requirements:

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-podcall

and update with::

   mamba update bioconductor-podcall

To create a new environment, run:

mamba create --name myenvname bioconductor-podcall

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-podcall:<tag>

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

Download stats

Link to this page

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