recipe bioconductor-macpet

Model based analysis for paired-end data

Homepage

https://bioconductor.org/packages/3.10/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

1.6.0-0, 1.4.0-1, 1.2.0-0

Depends

• bioconductor-biocparallel >=1.20.0,<1.21.0

• bioconductor-biostrings >=2.54.0,<2.55.0

• bioconductor-genomeinfodb >=1.22.0,<1.23.0

• bioconductor-genomicalignments >=1.22.0,<1.23.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-geoquery >=2.54.0,<2.55.0

• bioconductor-interactionset >=1.14.0,<1.15.0

• bioconductor-iranges >=2.20.0,<2.21.0

• bioconductor-rbowtie >=1.26.0,<1.27.0

• bioconductor-rsamtools >=2.2.0,<2.3.0

• bioconductor-rtracklayer >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• bioconductor-shortread >=1.44.0,<1.45.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• 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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