recipe bioconductor-circseqaligntk

A toolkit for end-to-end analysis of RNA-seq data for circular genomes

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-circseqaligntk/meta.yaml

CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.

package bioconductor-circseqaligntk

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rbowtie2:

>=2.8.0,<2.9.0

depends bioconductor-rhisat2:

>=1.18.0,<1.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-shortread:

>=1.60.0,<1.61.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-rlang:

depends r-tidyr:

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-circseqaligntk

and update with::

   mamba update bioconductor-circseqaligntk

To create a new environment, run:

mamba create --name myenvname bioconductor-circseqaligntk

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-circseqaligntk:<tag>

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

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