The sva package for removing batch effects and other unwanted variation in high-throughput experiments. - Jeffrey T. Leek; W. Evan Johnson; Hilary S. Parker; Andrew E. Jaffe; John D. Storey (Bioinform., 2012)

Gene set bagging for estimating the probability a statistically significant result will replicate. - Andrew E. Jaffe; John D. Storey; Hongkai Ji; Jeffrey T. Leek (BMC Bioinform., 2013)

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. - Martin J. Aryee; Andrew E. Jaffe; Héctor Corrada Bravo; Christine Ladd-Acosta; Andrew P. Feinberg; Kasper D. Hansen; Rafael A. Irizarry (Bioinform., 2014)

Polyester: simulating RNA-seq datasets with differential transcript expression. - Alyssa C. Frazee; Andrew E. Jaffe; Ben Langmead; Jeffrey T. Leek (Bioinform., 2015)

Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. - Andrew E. Jaffe; Thomas Hyde; Joel Kleinman; Daniel Weinbergern; Joshua Chenoweth; Ronald McKay; Jeffrey T. Leek; Carlo Colantuoni (BMC Bioinform., 2015)

regionReport: Interactive reports for region-based analyses. - Leonardo Collado-Torres; Andrew E. Jaffe; Jeffrey T. Leek (F1000Research, 2015)

Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. - Andrew E. Jaffe; Thomas Hyde; Joel Kleinman; Daniel R. Weinberger; Joshua Chenoweth; Ronald McKay; Jeffrey T. Leek; Carlo Colantuoni (BMC Bioinform., 2016)

Rail-RNA: scalable analysis of RNA-seq splicing and coverage. - Abhinav Nellore; Leonardo Collado-Torres; Andrew E. Jaffe; José Alquicira-Hernández; Christopher Wilks; Jacob Pritt; James Morton; Jeffrey T. Leek; Ben Langmead (Bioinform., 2017)

A Bayesian framework for multiple trait colocalization from summary association statistics. - Claudia Giambartolomei; Jimmy Zhenli Liu; Wen Zhang; Mads Hauberg; Huwenbo Shi; James Boocock; Joe Pickrell; Andrew E. Jaffe; CommonMind Consortium; Bogdan Pasaniuc; Panos Roussos (Bioinform., 2018)

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. - Nicholas J. Eagles; Emily E. Burke; Jacob Leonard; Brianna K. Barry; Joshua M. Stolz; Louise Huuki; BaDoi N. Phan; Violeta Larios Serrato; Everardo Gutiérrez-Millán; Israel Aguilar-Ordoñez; Andrew E. Jaffe; Leonardo Collado-Torres (BMC Bioinform., 2021)

Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. - Nicholas J. Eagles; Emily E. Burke; Jacob Leonard; Brianna K. Barry; Joshua M. Stolz; Louise Huuki; BaDoi N. Phan; Violeta Larios Serrato; Everardo Gutiérrez-Millán; Israel Aguilar-Ordoñez; Andrew E. Jaffe; Leonardo Collado-Torres (BMC Bioinform., 2021)

Predicting Mood Disorder Symptoms with Remotely Collected Videos Using an Interpretable Multimodal Dynamic Attention Fusion Network. - Tathagata Banerjee; Matthew Kollada; Pablo Gersberg; Oscar Rodriguez; Jane Tiller; Andrew E. Jaffe; John Reynders (CoRR, 2021)

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data. - Nicholas J. Eagles; Richard Wilton; Andrew E. Jaffe; Leonardo Collado-Torres (BMC Bioinform., 2023)