Package Recipe 'bioconductor-circseqaligntk'

recipe bioconductor-circseqaligntk

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

Homepage:: https://bioconductor.org/packages/3.20/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:

1.12.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rbowtie2 >=2.16.0,<2.17.0
on bioconductor-rhisat2 >=1.26.0,<1.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-shortread >=1.68.0,<1.69.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-ggplot2
on r-htmltools
on r-magrittr
on r-plotly
on r-r.utils
on r-rlang
on r-shiny
on r-shinyfiles
on r-shinyjs
on r-tidyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-circseqaligntk

to add into an existing workspace instead, run:

pixi add bioconductor-circseqaligntk

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-circseqaligntk

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-circseqaligntk

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-circseqaligntk:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-circseqaligntk/README.html)