recipe nanocount

Transcript abundance estimation from Nanopore *direct-RNA sequencing* datasets

Homepage:

https://github.com/a-slide/NanoCount/

Documentation:

https://a-slide.github.io/NanoCount/

License:

MIT

Recipe:

/nanocount/meta.yaml

Links:

doi: 10.1093/nar/gkab1129

NanoCount estimates transcripts abundance from Oxford Nanopore *direct-RNA sequencing* datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads

package nanocount

(downloads) docker_nanocount

versions:

1.0.0.post6-0

depends colorlog:

>=4.1.0

depends numpy:

>=1.19.4

depends pandas:

>=1.1.4

depends pysam:

>=0.16.0

depends python:

>=3.6

depends tqdm:

>=4.51.0

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 nanocount

and update with::

   mamba update nanocount

To create a new environment, run:

mamba create --name myenvname nanocount

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/nanocount:<tag>

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

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