recipe bioconductor-macpet

Model based analysis for paired-end data






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

(downloads) docker_bioconductor-macpet


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

Required By


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<tag>

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