Package Recipe 'bioconductor-duplexdiscoverer'

recipe bioconductor-duplexdiscoverer

Analysis of the data from RNA duplex probing experiments

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/DuplexDiscovereR.html
License:: GPL-3
Recipe:: /bioconductor-duplexdiscoverer/meta.yaml

DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.

package bioconductor-duplexdiscoverer¶

Versions:

1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-gviz >=1.54.0,<1.55.0
on bioconductor-interactionset >=1.38.0,<1.39.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-ggsci
on r-igraph
on r-purrr
on r-rlang
on r-scales
on r-stringr
on r-tibble
on r-tidyr
on r-vctrs

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-duplexdiscoverer

to add into an existing workspace instead, run:

pixi add bioconductor-duplexdiscoverer

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-duplexdiscoverer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-duplexdiscoverer

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-duplexdiscoverer:<tag>

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