Package Recipe 'bioconductor-genogam'

recipe bioconductor-genogam¶

This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package ‘mgcv’. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Estimation of dispersion and smoothing parameters is performed by cross-validation. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.

Homepage: https://bioconductor.org/packages/3.9/bioc/html/GenoGAM.html
License: GPL-2
Recipe: /bioconductor-genogam/meta.yaml
Links: biotools: genogam, doi: 10.1093/bioinformatics/btx150

package bioconductor-genogam¶

Versions: 2.0.2-0, 1.8.0-0, 1.6.0-0
Depends bioconductor-biocparallel: >=1.16.0,<1.17.0
Depends bioconductor-biostrings: >=2.50.0,<2.51.0
Depends bioconductor-delayedarray: >=0.8.0,<0.9.0
Depends bioconductor-deseq2: >=1.22.0,<1.23.0
Depends bioconductor-genomeinfodb: >=1.18.0,<1.19.0
Depends bioconductor-genomicalignments: >=1.18.0,<1.19.0
Depends bioconductor-genomicranges: >=1.34.0,<1.35.0
Depends bioconductor-hdf5array: >=1.10.0,<1.11.0
Depends bioconductor-iranges: >=2.16.0,<2.17.0
Depends bioconductor-rhdf5: >=2.26.0,<2.27.0
Depends bioconductor-rsamtools: >=1.34.0,<1.35.0
Depends bioconductor-s4vectors: >=0.20.0,<0.21.0
Depends bioconductor-summarizedexperiment: >=1.12.0,<1.13.0
Depends libgcc-ng: >=7.3.0
Depends libstdcxx-ng: >=7.3.0
Depends r-base: >=3.5.1,<3.5.2.0a0
Depends r-data.table: >=1.9.4
Depends r-futile.logger: >=1.4.1
Depends r-matrix: >=1.2-8
Depends r-rcpp: >=0.12.14
Depends r-rcpparmadillo
Depends r-sparseinv: >=0.1.1
Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-genogam

and update with:

conda update bioconductor-genogam

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-genogam:<tag>

(see bioconductor-genogam/tags for valid values for <tag>)

Link to this page¶

Render an 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-genogam/README.html)