recipe bioconductor-macpet

Model based analysis for paired-end data

Homepage:

https://bioconductor.org/packages/3.14/bioc/html/MACPET.html

License:

GPL-3

Recipe:

/bioconductor-macpet/meta.yaml

The MACPET package can be used for complete interaction analysis for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM format and separates the data into Self-ligated, Intra- and Inter-chromosomal PETs. Furthermore, MACPET breaks the genome into regions and applies 2D mixture models for identifying candidate peaks/binding sites using skewed generalized students-t distributions (SGT). It then uses a local poisson model for finding significant binding sites. Finally it runs an additive interaction-analysis model for calling for significant interactions between those peaks. MACPET is mainly written in C++, and it also supports the BiocParallel package.

package bioconductor-macpet

Versions:

1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1, 

1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

Depends:

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-biostrings >=2.62.0,<2.63.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicalignments >=1.30.0,<1.31.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-geoquery >=2.62.0,<2.63.0

• bioconductor-interactionset >=1.22.0,<1.23.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rbowtie >=1.34.0,<1.35.0

• bioconductor-rsamtools >=2.10.0,<2.11.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-shortread >=1.52.0,<1.53.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=10.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=10.3.0

• r-base >=4.1,<4.2.0a0

• r-bh >=1.66.0.1

• r-bigmemory >=4.5.33

• r-futile.logger >=1.4.3

• r-gtools >=3.8.1

• r-intervals >=0.15.1

• r-knitr >=1.23

• r-plyr >=1.8.4

• r-rcpp >=1.0.1

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-macpet

and update with:

conda update bioconductor-macpet

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-macpet:<tag>

(see bioconductor-macpet/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-macpet/README.html)