bioconda / packages / bioconductor-macpet 1.8.0

Model based analysis for paired-end data

Installers

Info: This package contains files in non-standard labels.

conda install

  • linux-64  v1.8.0
  • osx-64  v1.6.0
To install this package with conda run one of the following:
conda install -c bioconda bioconductor-macpet
conda install -c bioconda/label/gcc7 bioconductor-macpet

Description

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.

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