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

Nucleic acids research, 2014-12, Vol.42 (21), p.e161-e161

Leek, Jeffrey T

2014

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Capturing heterogeneity in gene expression studies by surrogate variable analysis

PLoS genetics, 2007-09, Vol.3 (9), p.1724-1735

2007

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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Nature protocols, 2016-09, Vol.11 (9), p.1650-1667

2016

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

BMC bioinformatics, 2011-11, Vol.12 (1), p.449-449, Article 449

2011

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

Proceedings of the National Academy of Sciences - PNAS, 2015-02, Vol.112 (6), p.1645-1646

2015

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Ballgown bridges the gap between transcriptome assembly and expression analysis

Nature biotechnology, 2015-03, Vol.33 (3), p.243-246

2015

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The sva package for removing batch effects and other unwanted variation in high-throughput experiments

Bioinformatics (Oxford, England), 2012-03, Vol.28 (6), p.882-883

2012

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Polyester: simulating RNA-seq datasets with differential transcript expression

Bioinformatics, 2015-09, Vol.31 (17), p.2778-2784

2015

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What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science

Perspectives on psychological science, 2016-07, Vol.11 (4), p.539-544

2016

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P values are just the tip of the iceberg

Nature (London), 2015-04, Vol.520 (7549), p.612

2015

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general framework for multiple testing dependence

Proceedings of the National Academy of Sciences - PNAS, 2008-12, Vol.105 (48), p.18718-18723

2008

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Methods for correcting inference based on outcomes predicted by machine learning

Proceedings of the National Academy of Sciences - PNAS, 2020-12, Vol.117 (48), p.30266-30275

2020

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recount3: summaries and queries for large-scale RNA-seq expression and splicing

Genome Biology, 2021-11, Vol.22 (1), p.323-323, Article 323

2021

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Reproducible RNA-seq analysis using recount2

Nature biotechnology, 2017-04, Vol.35 (4), p.319-321

2017

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Statistics: P values are just the tip of the iceberg

Nature (London), 2015-04, Vol.520 (7549), p.612-612

2015

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Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

Nature neuroscience, 2018-08, Vol.21 (8), p.1117-1125

2018

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Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

International journal of epidemiology, 2012-02, Vol.41 (1), p.200-209

2012

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Tackling the widespread and critical impact of batch effects in high-throughput data

Nature reviews. Genetics, 2010-10, Vol.11 (10), p.733-739

2010

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Addressing confounding artifacts in reconstruction of gene co-expression networks

Genome Biology, 2019-05, Vol.20 (1), p.94-94, Article 94

2019

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Transparency and reproducibility in artificial intelligence

Nature (London), 2020-10, Vol.586 (7829), p.E14-E16

2020

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Temporal dynamics and genetic control of transcription in the human prefrontal cortex

Nature (London), 2011-10, Vol.478 (7370), p.519-523

2011

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A direct approach to estimating false discovery rates conditional on covariates

PeerJ (San Francisco, CA), 2018-12, Vol.6, p.e6035-e6035, Article e6035

2018

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Test set bias affects reproducibility of gene signatures

Bioinformatics, 2015-07, Vol.31 (14), p.2318-2323

2015

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Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

International journal of epidemiology, 2012-02, Vol.41 (1), p.200-209

2012

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

Nucleic acids research, 2018-05, Vol.46 (9), p.e54-e54

2018

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

Capturing heterogeneity in gene expression studies by surrogate variable analysis

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

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

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

Ballgown bridges the gap between transcriptome assembly and expression analysis

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

Polyester: simulating RNA-seq datasets with differential transcript expression

What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science

P values are just the tip of the iceberg

general framework for multiple testing dependence

Methods for correcting inference based on outcomes predicted by machine learning

recount3: summaries and queries for large-scale RNA-seq expression and splicing

Reproducible RNA-seq analysis using recount2

Statistics: P values are just the tip of the iceberg

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

Tackling the widespread and critical impact of batch effects in high-throughput data

Addressing confounding artifacts in reconstruction of gene co-expression networks

Transparency and reproducibility in artificial intelligence

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

A direct approach to estimating false discovery rates conditional on covariates

Test set bias affects reproducibility of gene signatures

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

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

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