recipe bioconductor-wavcluster

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/wavClusteR.html

License:

GPL-2

Recipe:

/bioconductor-wavcluster/meta.yaml

Links:

biotools: wavcluster

The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).

package bioconductor-wavcluster

versions:

2.34.0-0,  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, 

2.34.0-0,  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,  2.11.0-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-foreach:

depends r-ggplot2:

depends r-hmisc:

depends r-mclust:

depends r-seqinr:

depends r-stringr:

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-wavcluster

and update with::

   mamba update bioconductor-wavcluster

To create a new environment, run:

mamba create --name myenvname bioconductor-wavcluster

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-wavcluster:<tag>

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

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