NBGOF-package: Goodness-of-Fit Tests and Model Diagnostics for Negative...

In gu-mi/NBGOF: Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data

Description

An R package for implementing goodness-of-fit tests for negative binomial (NB) distributions and NB dispersion models, with applications in RNA-Seq data analysis.

Details

This package can be used to test the goodness-of-fit of NB2, NBP or Poisson regression models. It can also be used to test the goodness-of-fit for a variety of negative binomial dispersion models in popular R/Bioconductor packages, including

• NBP dispersion model in the NBPSeq package (NBP)

• NBQ dispersion model in the NBPSeq package (NBQ)

• NB common dispersion model in the edgeR package (Common)

• NB genewise dispersion model in the edgeR package (Genewise)

• NB trended (non-parametric) dispersion model in the edgeR package (Trended)

• NB tagwise-common dispersion model in the edgeR package (Tagwise-Common)

• NB tagwise-trended dispersion model in the edgeR package (Tagwise-Trend)

Author(s)

Gu Mi <[e-mail]>, Yanming Di, Daniel Schafer

Maintainer: Gu Mi <https://github.com/gu-mi>

References

Mi, G, Di, Y, & Schafer, DW (2015). Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data. PLOS ONE, 10 (3).

Di Y, Schafer DW, Cumbie JS, and Chang JH (2011): "The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq", Statistical Applications in Genetics and Molecular Biology, 10 (1).

McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297.

Cox, DR, and Reid, N (1987). Parameter orthogonality and approximate conditional inference. Journal of the Royal Statistical Society Series B 49, 1-39.

See https://github.com/gu-mi/NBGOF/wiki/ for more details.

See Also

See nb.gof.v and nb.gof.m for examples on simulated datasets. See earthquake and arab for real data examples.

gu-mi/NBGOF documentation built on Oct. 25, 2020, 3:30 a.m.