:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-macpet' .. highlight: bash bioconductor-macpet =================== .. conda:recipe:: bioconductor-macpet :replaces_section_title: :noindex: 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. .. conda:package:: bioconductor-macpet |downloads_bioconductor-macpet| |docker_bioconductor-macpet| :versions: .. raw:: html
1.14.0-11.14.0-01.12.0-01.10.0-21.10.0-11.10.0-01.8.0-01.6.0-01.4.0-1 ``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`` .. raw:: html
:depends bioconductor-biocparallel: ``>=1.28.0,<1.29.0`` :depends bioconductor-biostrings: ``>=2.62.0,<2.63.0`` :depends bioconductor-genomeinfodb: ``>=1.30.0,<1.31.0`` :depends bioconductor-genomicalignments: ``>=1.30.0,<1.31.0`` :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0`` :depends bioconductor-geoquery: ``>=2.62.0,<2.63.0`` :depends bioconductor-interactionset: ``>=1.22.0,<1.23.0`` :depends bioconductor-iranges: ``>=2.28.0,<2.29.0`` :depends bioconductor-rbowtie: ``>=1.34.0,<1.35.0`` :depends bioconductor-rsamtools: ``>=2.10.0,<2.11.0`` :depends bioconductor-rtracklayer: ``>=1.54.0,<1.55.0`` :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0`` :depends bioconductor-shortread: ``>=1.52.0,<1.53.0`` :depends libblas: ``>=3.8.0,<4.0a0`` :depends libgcc-ng: ``>=10.3.0`` :depends liblapack: ``>=3.8.0,<4.0a0`` :depends libstdcxx-ng: ``>=10.3.0`` :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-bh: ``>=1.66.0.1`` :depends r-bigmemory: ``>=4.5.33`` :depends r-futile.logger: ``>=1.4.3`` :depends r-gtools: ``>=3.8.1`` :depends r-intervals: ``>=0.15.1`` :depends r-knitr: ``>=1.23`` :depends r-plyr: ``>=1.8.4`` :depends r-rcpp: ``>=1.0.1`` :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`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: (see `bioconductor-macpet/tags`_ for valid values for ````) .. |downloads_bioconductor-macpet| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-macpet.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-macpet :alt: (downloads) .. |docker_bioconductor-macpet| image:: https://quay.io/repository/biocontainers/bioconductor-macpet/status :target: https://quay.io/repository/biocontainers/bioconductor-macpet .. _`bioconductor-macpet/tags`: https://quay.io/repository/biocontainers/bioconductor-macpet?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-macpet/README.html