Jeffrey T Leek

Human splicing diversity across the Sequence Read Archive

The paper analyzes human RNA-seq data from the SRA to identify unannotated splicing junctions and their tissue-specific expression, creating a resource called intropolis.

A framework for RNA quality correction in differential expression analysis

This paper introduces a framework to correct RNA quality effects in differential expression analysis, showing improved replication rates in schizophrenia studies.

Is most published research really false?

The paper examines the issue of false discoveries in medical research, discusses definitions and evidence of false findings, and suggests tools to improve scientific practices.

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

Rail-dbGaP enables secure analysis of dbGaP-protected RNA-seq data in the cloud using Amazon Elastic MapReduce, with a spliced aligner tool and protocol for compliance with NIH guidelines.

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Rail-RNA efficiently and accurately aligns RNA-seq samples and generates coverage files, enabling population-level analysis of splicing and expression variation.

regionReport: Interactive reports for region-based analyses

regionReport generates interactive genomic reports with quality checks and templates for analyzing RNA-seq differential expression results.

Avoiding test set bias with rank-based prediction

The paper introduces a rank-based prediction framework to avoid test set bias by eliminating the need for cross-sample normalization, demonstrating its effectiveness with a breast cancer gene signature.

Flexible analysis of transcriptome assemblies with Ballgown

The paper introduces Ballgown, a tool for analyzing transcriptome assemblies from RNA-seq data, focusing on gene structure reconstruction and expression analysis.