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

(downloads) docker_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>)