recipe bioconductor-picb

piRNA Cluster Builder

Homepage:

https://bioconductor.org/packages/3.22/bioc/html/PICB.html

License:

CC0

Recipe:

/bioconductor-picb/meta.yaml

piRNAs (short for PIWI-interacting RNAs) and their PIWI protein partners play a key role in fertility and maintaining genome integrity by restricting mobile genetic elements (transposons) in germ cells. piRNAs originate from genomic regions known as piRNA clusters. The piRNA Cluster Builder (PICB) is a versatile toolkit designed to identify genomic regions with a high density of piRNAs. It constructs piRNA clusters through a stepwise integration of unique and multimapping piRNAs and offers wide-ranging parameter settings, supported by an optimization function that allows users to test different parameter combinations to tailor the analysis to their specific piRNA system. The output includes extensive metadata columns, enabling researchers to rank clusters and extract cluster characteristics.

package bioconductor-picb

(downloads) docker_bioconductor-picb

Versions:

1.2.0-0

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-iranges >=2.44.0,<2.45.0

  • on bioconductor-rsamtools >=2.26.0,<2.27.0

  • on bioconductor-s4vectors >=0.48.0,<0.49.0

  • on bioconductor-seqinfo >=1.0.0,<1.1.0

  • on r-base >=4.5,<4.6.0a0

  • on r-data.table

  • on r-dplyr

  • on r-openxlsx

  • on r-seqinr

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-picb

to add into an existing workspace instead, run:

pixi add bioconductor-picb

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-picb

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-picb

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-picb:<tag>

(see bioconductor-picb/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 install-with-bioconda 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-picb/README.html)