recipe bioconductor-duplexdiscoverer

Analysis of the data from RNA duplex probing experiments

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-duplexdiscoverer/meta.yaml

DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.

package bioconductor-duplexdiscoverer

versions:

1.0.0-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-gviz:

>=1.50.0,<1.51.0

depends bioconductor-interactionset:

>=1.34.0,<1.35.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggsci:

depends r-igraph:

depends r-purrr:

depends r-rlang:

depends r-scales:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-duplexdiscoverer

and update with::

   mamba update bioconductor-duplexdiscoverer

To create a new environment, run:

mamba create --name myenvname bioconductor-duplexdiscoverer

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-duplexdiscoverer:<tag>

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

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