Package Recipe 'bioconductor-triplex'

recipe bioconductor-triplex

Search and visualize intramolecular triplex-forming sequences in DNA

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/triplex.html
License:: BSD_2_clause + file LICENSE
Recipe:: /bioconductor-triplex/meta.yaml
Links:: biotools: triplex

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

package bioconductor-triplex¶

Versions:

1.50.0-0, 1.46.0-0, 1.42.0-0, 1.40.0-0, 1.38.0-1, 1.38.0-0, 1.34.0-2, 1.34.0-1, 1.34.0-0,

1.50.0-0, 1.46.0-0, 1.42.0-0, 1.40.0-0, 1.38.0-1, 1.38.0-0, 1.34.0-2, 1.34.0-1, 1.34.0-0, 1.32.0-0, 1.30.0-1, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-0

Depends:

on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-xvector >=0.50.0,<0.51.0
on bioconductor-xvector >=0.50.0,<0.51.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0

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-triplex

to add into an existing workspace instead, run:

pixi add bioconductor-triplex

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-triplex

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-triplex

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-triplex:<tag>

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