recipe bioconductor-macpet

Model based analysis for paired-end data

Homepage

https://bioconductor.org/packages/3.12/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

1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

Depends

• bioconductor-biocparallel >=1.24.0,<1.25.0

• bioconductor-biostrings >=2.58.0,<2.59.0

• bioconductor-genomeinfodb >=1.26.0,<1.27.0

• bioconductor-genomicalignments >=1.26.0,<1.27.0

• bioconductor-genomicranges >=1.42.0,<1.43.0

• bioconductor-geoquery >=2.58.0,<2.59.0

• bioconductor-interactionset >=1.18.0,<1.19.0

• bioconductor-iranges >=2.24.0,<2.25.0

• bioconductor-rbowtie >=1.30.0,<1.31.0

• bioconductor-rsamtools >=2.6.0,<2.7.0

• bioconductor-rtracklayer >=1.50.0,<1.51.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• bioconductor-shortread >=1.48.0,<1.49.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.5.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=7.5.0

• r-base >=4.0,<4.1.0a0

• 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 2. 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>)

Link to this page

Render an badge with the following MarkDown:

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