Jeffrey T. Leek

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derfinder: Software for annotation-agnostic RNA-seq differential expression analysis

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2015 .

Tools for Analyzing R Code the Tidy Way

Jeffrey T. Leek, D'agostino McGowan Lucy, Sean Kross, 2019, R J..

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

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2015, bioRxiv.

Discussion of "visualizing statistical models: Removing the blindfold"

Prasad Patil, Jeffrey T. Leek, 2015, Stat. Anal. Data Min..

Statistical Applications in Genetics and Molecular Biology The Joint Null Criterion for Multiple Hypothesis Tests

Jeffrey T. Leek, John D. Storey, J. Leek, 2011 .

Statistics: P values are just the tip of the iceberg

Jeffrey T. Leek, Roger D. Peng, J. Leek, 2015, Nature.

Gene set bagging for estimating the probability a statistically significant result will replicate

Andrew E. Jaffe, Jeffrey T. Leek, Hongkai Ji, 2013, BMC Bioinformatics.

Gene expression EDGE : extraction and analysis of differential gene expression

Jeffrey T. Leek, John D. Storey, John D. Storey, 2006 .

Analysis of Student Behavior Using the R Package crsra

John Muschelli, Jeffrey T. Leek, Aboozar Hadavand, 2019 .

A statistical definition for reproducibility and replicability

Prasad Patil, Jeffrey T. Leek, Roger D. Peng, 2016, bioRxiv.

Test set bias affects reproducibility of gene signatures

Prasad Patil, Benjamin Haibe-Kains, Jeffrey T. Leek, 2015, Bioinform..

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

Jeffrey T. Leek, 2014 .

Bioinformatics Applications Note Gene Expression the Sva Package for Removing Batch Effects and Other Unwanted Variation in High-throughput Experiments

Andrew E. Jaffe, Jeffrey T. Leek, W. Evan Johnson, 2022 .

On the Structure of Multiple Testing Procedures

Jeffrey T. Leek, John D. Storey, 2006 .

BatchQC: interactive software for evaluating sample and batch effects in genomic data

Benjamin Haibe-Kains, John Quackenbush, Jeffrey T. Leek, 2016, Bioinform..

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction

Jeffrey T. Leek, Sameer Chavan, Xiaoxin Xia, 2014, Bioinform..

The importance of transparency and reproducibility in artificial intelligence research

Trevor Hastie, Joelle Pineau, Robert Tibshirani, 2020, 2003.00898.

Gene expression anti-profiles as a basis for accurate universal cancer signatures

Vasyl Pihur, Matthew N. McCall, Rafael A. Irizarry, 2012, BMC Bioinformatics.

Ari: The Automated R Instructor pdf

John Muschelli, Jeffrey T. Leek, Sean Kross, 2020, R J..

Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression

Alyssa C. Frazee, Andrew E. Jaffe, Jeffrey T. Leek, 2014 .

Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression

Alyssa C. Frazee, Andrew E. Jaffe, Jeffrey T. Leek, 2014, bioRxiv.

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

Jeffrey T. Leek, Mehdi Pirooznia, Fernando S. Goes, 2013, Source Code for Biology and Medicine.

regionReport: Interactive reports for region-based analyses

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2015 .

recount-brain: a curated repository of human brain RNA-seq datasets metadata

Sean Davis, Leonardo Collado-Torres, Andrew E. Jaffe, 2019, bioRxiv.

Measuring the Contribution of Genomic Predictors to Improving Estimator Precision in Randomized trials

Prasad Patil, Jeffrey T. Leek, Michael Rosenblum, 2015, bioRxiv.

Avoiding test set bias with rank-based prediction

Prasad Patil, Benjamin Haibe-Kains, Jeffrey T. Leek, 2014, bioRxiv.

Rail-dbGaP: a protocol and tool for analyzing protected genomic data in a commercial cloud

Jeffrey T. Leek, Kasper Daniel Hansen, Abhinav Nellore, 2015 .

How to Share Data for Collaboration

Jeffrey T. Leek, Shannon E. Ellis, J. Leek, 2018, The American statistician.

Flexible analysis of transcriptome assemblies with Ballgown

Alyssa C. Frazee, Andrew E. Jaffe, Jeffrey T. Leek, 2014, bioRxiv.

Erratum to: Practical impacts of genomic data “cleaning” on biological discovery using surrogate variable analysis

Andrew E. Jaffe, Jeffrey T. Leek, Carlo Colantuoni, 2015, BMC Bioinformatics.

crsra: A package for Cleaning and Analyzing Coursera Research Export Data

Jeffrey T. Leek, Aboozar Hadavand, J. Leek, 2018, bioRxiv.

EDGE: extraction and analysis of differential gene expression

Jeffrey T. Leek, John D. Storey, Eva Monsen, 2006, Bioinform..

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

Alyssa C. Frazee, Jeffrey T. Leek, Ben Langmead, 2011, BMC Bioinformatics.

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

Jeffrey T. Leek, Christopher Wilks, Ben Langmead, 2016, Bioinform..

Is most published research really false?

Jeffrey T. Leek, Leah Ruth Jager, J. Leek, 2016, bioRxiv.

Opinion: Reproducible research can still be wrong: Adopting a prevention approach

Jeffrey T. Leek, Roger D. Peng, J. Leek, 2015, Proceedings of the National Academy of Sciences.

A statistical approach to selecting and confirming validation targets in -omics experiments

Jeffrey T. Leek, Margaret Taub, Jason L. Rasgon, 2012, BMC Bioinformatics.

A visual tool for defining reproducibility and replicability

Prasad Patil, Jeffrey T. Leek, Roger D. Peng, 2019, Nature Human Behaviour.

Personalized medicine: Keep a way open for tailored treatments

Jeffrey T. Leek, Roger D. Peng, R. Reeves Anderson, 2012, Nature.

Removing batch effects for prediction problems with frozen surrogate variable analysis

Jeffrey T. Leek, Héctor Corrada Bravo, Hilary S. Parker, 2013, PeerJ.

A Significance Method for Time Course Microarray Experiments Applied to Two Human Studies

Jeffrey T. Leek, Ronald W. Davis, John D. Storey, 2004 .

The tspair package for finding top scoring pair classifiers in R

Jeffrey T. Leek, J. Leek, 2009, Bioinform..

A computationally efficient modular optimal discovery procedure

Jeffrey T. Leek, John D. Storey, John D. Storey, 2011, Bioinform..

RNA-seq transcript quantification from reduced-representation data in recount2

Leonardo Collado-Torres, Jeffrey T. Leek, Abhinav Nellore, 2018, bioRxiv.

Post-prediction Inference

Siruo Wang, Jeffrey T. Leek, Tyler H. McCormick, 2020, bioRxiv.

Cloud-scale RNA-sequencing differential

Jeffrey T. Leek, Kasper Daniel Hansen, Ben Langmead, 2010 .

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2016, bioRxiv.

Diagnosing Data Analytic Problems in the Classroom

Jeffrey T. Leek, Roger D. Peng, Eric Bridgeford, 2021 .

Diversifying the Genomic Data Science Research Community

AZ, Baltimore, Michael C. Schatz, 2022 .

Linking open-source code commits and MOOC grades to evaluate massive online open peer review pdf

Siruo Wang, Jeffrey T. Leek, Aboozar Hadavand, 2021, ArXiv.

Human splicing diversity across the Sequence Read Archive

Siruo Wang, Leonardo Collado-Torres, Andrew E. Jaffe, 2016, bioRxiv.

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

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2015, bioRxiv.

Practical impacts of genomic data “cleaning” on biological discovery using surrogate variable analysis

Andrew E. Jaffe, Jeffrey T. Leek, Carlo Colantuoni, 2015, BMC Bioinformatics.

A regression framework for the proportion of true null hypotheses

Jeffrey T. Leek, Simina M. Boca, 2017 .

A glass half full interpretation of the replicability of psychological science

Prasad Patil, Jeffrey T. Leek, Roger D. Peng, 2015, 1509.08968.

Improving the value of public RNA-seq expression data by phenotype prediction

Leonardo Collado-Torres, Jeffrey T. Leek, Shannon E. Ellis, 2017 .

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2015, bioRxiv.

Addressing confounding artifacts in reconstruction of gene co-expression networks

Michael C. Schatz, Alexis Battle, Andrew E. Jaffe, 2017 .

Developmental regulation of human cortex transcription and its clinical relevance at base resolution

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2014, Nature Neuroscience.

Differential expression analysis of RNA-seq data at single-base resolution

Rafael A. Irizarry, Alyssa C. Frazee, Jeffrey T. Leek, 2014, Biostatistics.

Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study

Ronald G. Tompkins, Jeffrey T. Leek, John D. Storey, 2011, PLoS medicine.

Addressing confounding artifacts in reconstruction of gene co-expression networks

Michael C. Schatz, Alexis Battle, Andrew E. Jaffe, 2018, Genome Biology.

Erratum: EDGE: Extraction and analysis of differential gene expression (Bioinformatics (2006) vol. 22 (4) (507-508))

Jeffrey T. Leek, John D. Storey, Eva Monsen, 2006 .