- recipe bioconductor-wavcluster
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/wavClusteR.html
- License:
GPL-2
- Recipe:
- 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:
2.32.0-0
,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
,2.32.0-0
,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
>=0.44.0,<0.45.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-genomicfeatures
>=1.50.0,<1.51.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-rsamtools
>=2.14.0,<2.15.0
bioconductor-rtracklayer
>=1.58.0,<1.59.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-wavcluster
and update with:
conda update bioconductor-wavcluster
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-wavcluster:<tag>
(see bioconductor-wavcluster/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-wavcluster/README.html)