Package Recipe 'bioconductor-rnamodr'

recipe bioconductor-rnamodr

Detection of post-transcriptional modifications in high throughput sequencing data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/RNAmodR.html
License:: Artistic-2.0
Recipe:: /bioconductor-rnamodr/meta.yaml

RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.

package bioconductor-rnamodr¶

Versions:

1.24.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.2-0, 1.4.0-0,

1.24.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.2-0, 1.4.0-0, 1.2.1-0, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-gviz >=1.54.0,<1.55.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-modstrings >=1.26.0,<1.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-txdbmaker >=1.6.0,<1.7.0
on r-base >=4.5,<4.6.0a0
on r-colorramps
on r-ggplot2
on r-matrixstats
on r-rcolorbrewer
on r-reshape2
on r-rocr

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-rnamodr

to add into an existing workspace instead, run:

pixi add bioconductor-rnamodr

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-rnamodr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rnamodr

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-rnamodr:<tag>

(see bioconductor-rnamodr/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-rnamodr/README.html)