Jeffrey Leek

Flexible expressed region analysis for RNA-seq with derfinder

The paper introduces derfinder, a tool for RNA-seq analysis that identifies differentially expressed regions at single base resolution without relying on gene annotations, showing it works well with incomplete annotations and large datasets.

recount: A large-scale resource of analysis-ready RNA-seq expression data

recount provides a large-scale, processed RNA-seq resource with tools for analysis, including differential expression and meta-analysis, using data from the Sequence Read Archive.

Polyester: simulating RNA-seq datasets with differential transcript expression

Polyester simulates RNA-seq data with differential transcript expression to evaluate statistical methods for differential expression analysis.

svaseq: removing batch effects and other unwanted noise from sequencing data

svaseq removes batch effects and other unwanted noise from sequencing data using surrogate variable analysis and supervised sva.