Find top confident effect sizes 


Confident effect sizes based on the edgeR QuasiLikelihood method, both linear and nonlinear 

Confident log2 fold changes using limma's treat function, linear effects only 

Confident nonlinear effect sizes using limma 

General purpose function to find sets of discoveries for a range of effect sizes, controlling FDR 

Diagnostic plots 

Top confident effect sizes plot 

A plot to compare two rankings 

Meanexpression vs effect size plot 

Nonlinear effect size definitionsThese can be used with edger_confects or limma_nonlinear_confects. 

Ratio of contrasts effect. 

Simple linear contrast effect. 

Goodman and Kruskall's gamma, Yule's Q 

Adapt an effect size object to work with coefficients estimated from log2 transformed data or with a log2 link function 

Standarddeviation of a set of coefficients as effect size 


Shift of mass effect 
Find top confident effect sizes for groups of featuresFor differential splicing, or shifts of transcript start or end. 

Group confects (differential exon usage, etc) 

Group effect size definitionsThese can be used with edger_group_confects or limma_group_confects. 

Group effect for differential splicing 


Group effect for shifts in 5' or 3' end usage 