recipe bioconductor-pqsfinder

Identification of potential quadruplex forming sequences

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/pqsfinder.html

License:

BSD_2_clause + file LICENSE

Recipe:

/bioconductor-pqsfinder/meta.yaml

Links:

biotools: pqsfinder, doi: 10.1093/bioinformatics/btv272

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

package bioconductor-pqsfinder

versions:

2.22.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.10.1-1,  2.10.1-0,  2.10.0-0,  2.8.0-0, 

2.22.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.10.1-1,  2.10.1-0,  2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.4.0-0,  2.2.0-0,  2.0.1-0,  1.10.0-0,  1.8.0-0,  1.6.3-0

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 libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-bh:

>=1.78.0

depends r-rcpp:

>=0.12.3

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-pqsfinder

and update with::

   mamba update bioconductor-pqsfinder

To create a new environment, run:

mamba create --name myenvname bioconductor-pqsfinder

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-pqsfinder:<tag>

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

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