- recipe bioconductor-ribodipa
Differential pattern analysis for Ribo-seq data
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/RiboDiPA.html
- License:
LGPL (>= 3)
- Recipe:
This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.
- package bioconductor-ribodipa¶
- versions:
1.14.0-0,1.10.0-0,1.8.0-0,1.6.0-1,1.6.0-0,1.2.0-2,1.2.0-1,1.2.0-0,1.0.0-0- depends bioconductor-biocfilecache:
>=2.14.0,<2.15.0- depends bioconductor-biocfilecache:
>=2.14.0,<2.15.0a0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0a0- depends bioconductor-deseq2:
>=1.46.0,<1.47.0- depends bioconductor-deseq2:
>=1.46.0,<1.47.0a0- depends bioconductor-genomicalignments:
>=1.42.0,<1.43.0- depends bioconductor-genomicalignments:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicfeatures:
>=1.58.0,<1.59.0- depends bioconductor-genomicfeatures:
>=1.58.0,<1.59.0a0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0a0- depends bioconductor-iranges:
>=2.40.0,<2.41.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0a0- depends bioconductor-qvalue:
>=2.38.0,<2.39.0- depends bioconductor-qvalue:
>=2.38.0,<2.39.0a0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-txdbmaker:
>=1.2.0,<1.3.0- depends bioconductor-txdbmaker:
>=1.2.0,<1.3.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=13- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx:
>=13- depends r-base:
>=4.4,<4.5.0a0- depends r-data.table:
- depends r-doparallel:
- depends r-elitism:
- depends r-foreach:
- depends r-ggplot2:
- depends r-matrixstats:
- depends r-rcpp:
>=1.0.2- depends r-reldist:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-ribodipa and update with:: mamba update bioconductor-ribodipa
To create a new environment, run:
mamba create --name myenvname bioconductor-ribodipa
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-ribodipa:<tag> (see `bioconductor-ribodipa/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-ribodipa/README.html)
