recipe bioconductor-ribosomeprofilingqc

Ribosome Profiling Quality Control

Homepage:

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

License:

GPL (>=3) + file LICENSE

Recipe:

/bioconductor-ribosomeprofilingqc/meta.yaml

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

package bioconductor-ribosomeprofilingqc

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.1-0,  1.2.0-0,  1.0.1-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-edaseq:

>=2.36.0,<2.37.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-motifstack:

>=1.46.0,<1.47.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsubread:

>=2.16.0,<2.17.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-ruvseq:

>=1.36.0,<1.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-xvector:

>=0.42.0,<0.43.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-ggfittext:

depends r-ggplot2:

depends r-ggrepel:

depends r-scales:

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-ribosomeprofilingqc

and update with::

   mamba update bioconductor-ribosomeprofilingqc

To create a new environment, run:

mamba create --name myenvname bioconductor-ribosomeprofilingqc

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-ribosomeprofilingqc:<tag>

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

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