recipe trumicount

For NGS experiments using unique molecular identifiers (UMIs), molecules that are lost entirely during sequencing cause under- estimation of the molecule count, and amplification artifacts like PCR chimeras cause over-estimation. TRUmiCount corrects UMI data for both types of errors, thus improving the accuracy of measured molecule counts considerably.

Homepage:

https://cibiv.github.io/trumicount/

Developer docs:

https://github.com/Cibiv/trumicount

License:

AGPL / AGPL-3.0

Recipe:

/trumicount/meta.yaml

package trumicount

(downloads) docker_trumicount

versions:
0.9.14-3,  0.9.14-2,  0.9.14-1,  0.9.14-0,  0.9.13-3,  0.9.13-2,  0.9.13-1,  0.9.13-0,  0.9.12-0, 

0.9.14-3,  0.9.14-2,  0.9.14-1,  0.9.14-0,  0.9.13-3,  0.9.13-2,  0.9.13-1,  0.9.13-0,  0.9.12-0,  0.9.11.1-0,  0.9.11-1,  0.9.10-1,  0.9.9.3-1,  0.9.9.3-0

depends gawk:

>=4.0.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-docopt:

depends r-gwpcr:

>=0.9.10

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 trumicount

and update with::

   mamba update trumicount

To create a new environment, run:

mamba create --name myenvname trumicount

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/trumicount:<tag>

(see `trumicount/tags`_ for valid values for ``<tag>``)

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Link to this page

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