recipe r-noisyr

Quantifies and removes technical noise from high-throughput sequencing data. Two approaches are used, one based on the count matrix, and one using the alignment BAM files directly. Contains several options for every step of the process, as well as tools to quality check and assess the stability of output.

Homepage:

https://github.com/Core-Bioinformatics/noisyR

License:

GPL2 / GPL-2.0-only

Recipe:

/r-noisyr/meta.yaml

package r-noisyr

(downloads) docker_r-noisyr

versions:

1.0.0-3,  1.0.0-2,  1.0.0-1,  1.0.0-0

depends bioconductor-genomicranges:

depends bioconductor-iranges:

depends bioconductor-preprocesscore:

depends bioconductor-rsamtools:

depends r-base:

>=4.4,<4.5.0a0

depends r-doparallel:

depends r-dplyr:

depends r-foreach:

depends r-ggplot2:

depends r-magrittr:

depends r-philentropy:

depends r-tibble:

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 r-noisyr

and update with::

   mamba update r-noisyr

To create a new environment, run:

mamba create --name myenvname r-noisyr

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/r-noisyr:<tag>

(see `r-noisyr/tags`_ for valid values for ``<tag>``)

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Link to this page

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