Andrew E. Jaffe

发表

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

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

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

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

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

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

SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses

Joshua Stolz, Andrew E. Jaffe, Nick Eagles, 2020 .

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

Alan J. Cross, Leonardo Collado-Torres, Andrew E. Jaffe, 2018, bioRxiv.

dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues

Andrew E. Jaffe, BaDoi N Phan, BaDoi N. Phan, 2019, bioRxiv.

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 .

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

Leonardo Collado-Torres, Andrew E. Jaffe, Kasper Daniel Hansen, 2016, bioRxiv.

GEUVADIS expressed regions coverage matrix

Andrew E. Jaffe, Ben Langmead, Collado-Torres Leonardo, 2015 .

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

Rafael A. Irizarry, Andrew P. Feinberg, Martin J. Aryee, 2014, Bioinform..

Correcting for cell-type heterogeneity in epigenome-wide association studies: premature analyses and conclusions

Devin C. Koestler, Rafael A. Irizarry, Andrew E. Teschendorff, 2017, bioRxiv.

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.

regionReport: Interactive reports for region-based analyses

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

A Bayesian Framework for Multiple Trait Colocalization from Summary Association Statistics

Wen Zhang, Joseph K. Pickrell, Andrew E. Jaffe, 2017, bioRxiv.

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

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

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.

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

Leonardo Collado-Torres, Andrew E. Jaffe, Louise A. Huuki, 2020, BMC Bioinformatics.

Flexible expressed region analysis for RNA-seq with derfinder

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

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

Leonardo Collado-Torres, Andrew E. Jaffe, Emily E. Burke, 2021, BMC Bioinform..

Human splicing diversity across the Sequence Read Archive

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

Prefrontal Coexpression of Schizophrenia Risk Genes Is Associated With Treatment Response in Patients

Andrew E. Jaffe, Alessandro Bertolino, Giulio Pergola, 2019, Biological Psychiatry.

BrainSeq: Neurogenomics to Drive Novel Target Discovery for Neuropsychiatric Disorders

Brian J. Eastwood, Andrew E. Jaffe, Daniel R. Weinberger, 2015, Neuron.

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.

Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

Leonardo Collado-Torres, Andrew E. Jaffe, Juan A. Botía, 2020, Science Advances.

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.

Addressing confounding artifacts in reconstruction of gene co-expression networks

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