recipe bioconductor-triplex

Search and visualize intramolecular triplex-forming sequences in DNA

Homepage:

https://bioconductor.org/packages/3.18/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:

1.46.0-0,  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, 

1.46.0-0,  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 bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0a0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends bioconductor-xvector:

>=0.46.0,<0.47.0

depends bioconductor-xvector:

>=0.46.0,<0.47.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.4,<4.5.0a0

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-triplex

and update with::

   mamba update bioconductor-triplex

To create a new environment, run:

mamba create --name myenvname bioconductor-triplex

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-triplex:<tag>

(see `bioconductor-triplex/tags`_ for valid values for ``<tag>``)

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