- recipe bioconductor-macpet
Model based analysis for paired-end data
- Homepage:
https://bioconductor.org/packages/3.14/bioc/html/MACPET.html
- License:
GPL-3
- Recipe:
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:
1.14.0-1
,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
,1.14.0-1
,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
- Depends:
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicalignments
>=1.30.0,<1.31.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-geoquery
>=2.62.0,<2.63.0
bioconductor-interactionset
>=1.22.0,<1.23.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rbowtie
>=1.34.0,<1.35.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-shortread
>=1.52.0,<1.53.0
libblas
>=3.8.0,<4.0a0
libgcc-ng
>=10.3.0
liblapack
>=3.8.0,<4.0a0
libstdcxx-ng
>=10.3.0
r-base
>=4.1,<4.2.0a0
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 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-macpet/README.html)