R/scNORM: A BioConductor package for normalization of single-cell RNA-seq data. Primary report: Bacher et al., Nature Methods, 2017.
R/rvalues: An R package for ranking and selection in large-scale inference.
Primary report: Henderson and Newton, Journal of the Royal Statistical Society, 2016; also at
R/Rolemodel: An R package for multivariate gene-set analysis. Primary report:
Wang et al., The Annals of Applied Statistics, 2015 .
- R/dod: An R package for deploying inference in a double over-dispersion model for a particlar class of sequence count data. Version 2.0, July 2013.
Pei et al., Biostatistics, 2013.
An R package for deploying meta-analysis
in a class of RNA interference studies.
Version 1.0, December 2012.
Primary report: Hao et al., PLoS Computational Biology, 2013.
An R package for computing gamma ranking probabilities.
With Z_1, Z_2, ... , Z_k equal to independent Gamma-distributed
random variables with positive integer shapes a_1, a_2, ..., a_k
and positive rates lambda_1, lambda_2, ..., lambda_k, returned by
the main function is
the (log) probability P[Z_1> Z_2 > ... > Z_k ]
allez: An R package for calibrating gene-set
summary statistics derived from gene-level genomic data. Utilizes
either Gene Ontology (GO) or KEGG gene sets, and various gene-level
data formats. Primary report: Newton et al., The Annals of Applied Statistics, 2007.
EBarrays: A Bioconductor package implementing parametric empirical Bayesian analysis for differential gene expression. Primary Report: Newton et al., Journal of Computational Biology, 2001.