Package Recipe 'rnaframework'

recipe rnaframework

Toolkit for the analysis of RNA structures and post-transcriptional modifications from HTS data

Homepage:: https://github.com/dincarnato/RNAFramework
Documentation:: https://rnaframework-docs.readthedocs.io/
License:: GPL3 / GPL-3.0-or-later
Recipe:: /rnaframework/meta.yaml
Links:: doi: 10.1093/nar/gky486

RNA Framework is a modular toolkit designed to handle RNA structure probing and post-transcriptional modifications mapping from high-throughput sequencing data. It supports transcriptome-scale analysis of RNA secondary structure using protocols such as CIRS-seq, SHAPE-seq, Structure-seq, DMS-seq, PARS, SHAPE-MaP, and DMS-MaPseq, as well as mapping of post-transcriptional modifications (Ψ, m1A, m6A, m5C, hm5C, 2'-OMe).

Key features:: - Automatic reference transcriptome creation (rf-index) - Read preprocessing, adapter trimming, and mapping (rf-map) - Per-base RT-stop/mutation counting and coverage (rf-count) - Reactivity scoring and whole-transcriptome normalization (rf-norm) - RNA secondary structure prediction with probing data (rf-fold) - RNA-RNA interaction mapping (rf-duplex) - Post-transcriptional modification calling (rf-modcall) - Peak calling for RNA immunoprecipitation data (rf-peakcall)

package rnaframework¶

Versions:

2.9.6-1, 2.9.6-0

Depends:

on bedtools >=2.31
on bowtie >=1.2.3
on bowtie2 >=2.3.5
on cutadapt >=2.1
on perl >=5.12
on perl >=5.32.1,<6.0a0 *_perl5
on perl-termreadkey
on r-base >=4.4,<4.6
on r-ggplot2 >=3.5.2
on r-patchwork >=1.3.2
on r-rcolorbrewer >=1.1_3
on rnastructure >=6.4
on samtools >=1.15
on viennarna >=2.5.0

Additional platforms:

linux-aarch64, osx-arm64

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 rnaframework

to add into an existing workspace instead, run:

pixi add rnaframework

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 rnaframework

Alternatively, to install into a new environment, run:

conda create -n envname rnaframework

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/rnaframework:<tag>

(see rnaframework/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/rnaframework/README.html)