- recipe bioconductor-genogam
A GAM based framework for analysis of ChIP-Seq data
- Homepage:
https://bioconductor.org/packages/3.14/bioc/html/GenoGAM.html
- License:
GPL-2
- Recipe:
- Links:
biotools: genogam, doi: 10.1093/bioinformatics/btx150
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.
- package bioconductor-genogam¶
-
- Versions:
2.11.0-1
,2.11.0-0
,2.10.0-0
,2.8.0-1
,2.8.0-0
,2.6.0-0
,2.4.0-0
,2.2.0-1
,2.0.2-0
,2.11.0-1
,2.11.0-0
,2.10.0-0
,2.8.0-1
,2.8.0-0
,2.6.0-0
,2.4.0-0
,2.2.0-1
,2.0.2-0
,1.8.0-0
,1.6.0-0
- Depends:
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-delayedarray
>=0.20.0,<0.21.0
bioconductor-deseq2
>=1.34.0,<1.35.0
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-hdf5array
>=1.22.0,<1.23.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rhdf5
>=2.38.0,<2.39.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
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-data.table
>=1.9.4
r-futile.logger
>=1.4.1
r-matrix
>=1.2-8
r-rcpp
>=0.12.14
r-sparseinv
>=0.1.1
- Required By:
Installation
With an activated Bioconda channel (see 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-genogam/README.html)