recipe bioconductor-segmentseq

Methods for identifying small RNA loci from high-throughput sequencing data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/segmentSeq.html

License:

GPL-3

Recipe:

/bioconductor-segmentseq/meta.yaml

High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.

package bioconductor-segmentseq

versions:

2.36.0-0,  2.32.0-0,  2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.22.0-0,  2.20.0-0,  2.18.0-1, 

2.36.0-0,  2.32.0-0,  2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.22.0-0,  2.20.0-0,  2.18.0-1,  2.16.0-0,  2.14.0-0,  2.12.0-0,  2.10.0-0

depends bioconductor-bayseq:

>=2.36.0,<2.37.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-shortread:

>=1.60.0,<1.61.0

depends r-abind:

depends r-base:

>=4.3,<4.4.0a0

requirements:

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-segmentseq

and update with::

   mamba update bioconductor-segmentseq

To create a new environment, run:

mamba create --name myenvname bioconductor-segmentseq

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-segmentseq:<tag>

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

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