GenoGAM 1.8.0

A GAM based framework for analysis of ChIP-Seq data

Released Sep 14, 2017 by Georg Stricker

This package cannot yet be used with Renjin it depends on other packages which are not available: data.table 1.11.4


data.table 1.11.4 DESeq2 1.20.0 GenomeInfoDb 1.16.0 futile.logger S4Vectors 0.18.3 BiocParallel 1.14.2 SummarizedExperiment 1.10.1 Rsamtools 1.32.3 reshape2 1.4.3 GenomicAlignments 1.16.0 Biostrings 2.48.0 GenomicRanges 1.32.6 IRanges 2.14.10 mgcv 1.8-24

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.



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