<commit_before>---
layout: page
title: Papers
---

More info on my [Google Scholar profile](http://scholar.google.com/citations?user=HI-I6C0AAAAJ&hl=en&oi=ao)


### Preprints


* <NAME>, <NAME>, <NAME>, Leek JT (2014) _Avoiding test set bias with rank-based predictors_ bioRxiv doi:10.1101/005983 [[link]](http://biorxiv.org/content/early/2014/06/06/005983) [[analysis code]](https://github.com/prpatil/testsetbias)

* <NAME>, <NAME>, <NAME>, Leek JT (2014) _Polyester: simulating RNA-seq dataets with differential expression_ bioRxiv doi: 10.1101/006015 [[link]](http://biorxiv.org/content/early/2014/06/06/006015) [[software]](https://github.com/alyssafrazee/polyester) [[analysis code]](https://github.com/alyssafrazee/polyester_code)

* <NAME>, <NAME>, <NAME>, <NAME>, Salzberg SL, Leek JT (2014) _Flexible isoform-level differential expression analysis with Ballgown_ bioRxiv doi: 10.1101/003665 [[link]](http://biorxiv.org/content/early/2014/03/30/003665) [[software]](https://github.com/alyssafrazee/ballgown) [[analysis code]](https://github.com/alyssafrazee/ballgown_code) [[geuvadis data]](https://www.dropbox.com/s/kp5th9hgkq8ckom/geuvadisbg.rda)

* <NAME>, <NAME>, Leek JT (2014) _A randomized trial in a massive online open course shows people don't know what a statistically significant relationship looks like, but they can learn_  arXiv:1404.5358 [[link]](http://arxiv.org/abs/1404.5358) [[p-value shiny app]](http://glimmer.rstudio.com/afisher/EDA/)


### 2014

* Leek JT (2014) _svaseq: removing batch effects and other unwanted noise from sequencing data_ Nucl. Acids Res. doi: 10.1093/nar/gku864 [[paper]](http://nar.oxfordjournals.org/content/early/2014/10/07/nar.gku864.full?keytype=ref&ijkey=Rq9NTea3ZraBKMQ) [[preprint]](http://biorxiv.org/content/early/2014/06/25/006585) [[software]](http://www.bioconductor.org/packages/devel/bioc/html/sva.html) [[analysis code]](https://github.com/jtleek/svaseq)

* <NAME>S, <NAME>, <NAME>. (2014) _Removing batch effects for prediction problems with frozen surrogate variable analysis._ PeerJ 2:e561 [[paper]](http://dx.doi.org/10.7717/peerj.561) [[preprint]](http://arxiv.org/abs/1301.3947) [[software]](http://www.bioconductor.org/packages/devel/bioc/html/sva.html)

* <NAME>S, Leek JT, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME> (2014) _Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction_ [[link]](http://bioinformatics.oxfordjournals.org/content/early/2014/06/06/bioinformatics.btu375.long) [[analysis code]](https://sourceforge.net/projects/psva) [[software]](http://www.bioconductor.org/packages/devel/bioc/html/sva.html)

* <NAME>, Severance EG, Leek JT, Gressitt KL, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. (2014) _Inflammatory molecular signature associated with infectious agents in psychosis_. Scizhophrenia Bulletin doi: 10.1093/schbul/sbu052 [[link]](http://schizophreniabulletin.oxfordjournals.org/content/early/2014/04/16/schbul.sbu052.full)

* <NAME>, <NAME>, <NAME>, <NAME>, Leek JT (2014) _Differential expression analysis of RNA-seq data at single-base resolution_ Biostatistics 10.1093/biostatistics/kxt053 [[link]](http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.short)[[software]](https://github.com/alyssafrazee/derfinder) [[newer software]](https://github.com/lcolladotor/derfinder)

* <NAME>, Leek JT (2014) _An estimate of the science-wise false discovery rate and application to the top medical literature_ Biostatistics 15(1) 1-12 [[link]](http://biostatistics.oxfordjournals.org/content/15/1/1.short)[[blog post]](http://simplystatistics.org/2013/09/25/is-most-science-false-the-titans-weigh-in/) [[code]](https://github.com/jtleek/swfdr) [data](https://github.com/jtleek/swfdr/blob/master/pvalueData.rda) [[preprint]](http://arxiv.org/pdf/1301.3718.pdf)
<commit_msg>updated papers<commit_after>---
layout: page
title: Papers
---

More info on my [Google Scholar profile](http://scholar.google.com/citations?user=HI-I6C0AAAAJ&hl=en&oi=ao)


### Preprints


* <NAME>, <NAME>, <NAME>, Leek JT (2014) _Avoiding test set bias with rank-based predictors_ bioRxiv doi:10.1101/005983 [[link]](http://biorxiv.org/content/early/2014/06/06/005983) [[analysis code]](https://github.com/prpatil/testsetbias)

* <NAME>, <NAME>, <NAME>, Leek JT (2014) _Polyester: simulating RNA-seq dataets with differential expression_ bioRxiv doi: 10.1101/006015 [[link]](http://biorxiv.org/content/early/2014/06/06/006015) [[software]](https://github.com/alyssafrazee/polyester) [[analysis code]](https://github.com/alyssafrazee/polyester_code)

* <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, Leek JT (2014) _Flexible isoform-level differential expression analysis with Ballgown_ bioRxiv doi: 10.1101/003665 [[link]](http://biorxiv.org/content/early/2014/03/30/003665) [[software]](https://github.com/alyssafrazee/ballgown) [[analysis code]](https://github.com/alyssafrazee/ballgown_code) [[geuvadis data]](https://www.dropbox.com/s/kp5th9hgkq8ckom/geuvadisbg.rda)



### 2014

* <NAME>, <NAME>, Leek JT (2014) _A randomized trial in a massive online open course shows people don't know what a statistically significant relationship looks like, but they can learn_ PeerJ 2:e589 DOI 10.7717/peerj.589 [[paper]](https://peerj.com/articles/589/) [[preprint]](http://arxiv.org/abs/1404.5358) [[p-value shiny app]](http://glimmer.rstudio.com/afisher/EDA/)


* Leek JT (2014) _svaseq: removing batch effects and other unwanted noise from sequencing data_ Nucl. Acids Res. doi: 10.1093/nar/gku864 [[paper]](http://nar.oxfordjournals.org/content/early/2014/10/07/nar.gku864.full?keytype=ref&ijkey=Rq9NTea3ZraBKMQ) [[preprint]](http://biorxiv.org/content/early/2014/06/25/006585) [[software]](http://www.bioconductor.org/packages/devel/bioc/html/sva.html) [[analysis code]](https://github.com/jtleek/svaseq)

* <NAME>, <NAME>, Leek JT. (2014) _Removing batch effects for prediction problems with frozen surrogate variable analysis._ PeerJ 2:e561 DOI 10.7717/peerj.561 [[paper]](http://dx.doi.org/10.7717/peerj.561) [[preprint]](http://arxiv.org/abs/1301.3947) [[software]](http://www.bioconductor.org/packages/devel/bioc/html/sva.html)

* <NAME>, Leek JT, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME> (2014) _Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction_ [[link]](http://bioinformatics.oxfordjournals.org/content/early/2014/06/06/bioinformatics.btu375.long) [[analysis code]](https://sourceforge.net/projects/psva) [[software]](http://www.bioconductor.org/packages/devel/bioc/html/sva.html)

* <NAME>, <NAME>, Leek JT, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. (2014) _Inflammatory molecular signature associated with infectious agents in psychosis_. Scizhophrenia Bulletin doi: 10.1093/schbul/sbu052 [[link]](http://schizophreniabulletin.oxfordjournals.org/content/early/2014/04/16/schbul.sbu052.full)

* <NAME>, <NAME>, <NAME>D, <NAME>, Leek JT (2014) _Differential expression analysis of RNA-seq data at single-base resolution_ Biostatistics 10.1093/biostatistics/kxt053 [[link]](http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.short)[[software]](https://github.com/alyssafrazee/derfinder) [[newer software]](https://github.com/lcolladotor/derfinder)

* <NAME>, Leek JT (2014) _An estimate of the science-wise false discovery rate and application to the top medical literature_ Biostatistics 15(1) 1-12 [[link]](http://biostatistics.oxfordjournals.org/content/15/1/1.short)[[blog post]](http://simplystatistics.org/2013/09/25/is-most-science-false-the-titans-weigh-in/) [[code]](https://github.com/jtleek/swfdr) [data](https://github.com/jtleek/swfdr/blob/master/pvalueData.rda) [[preprint]](http://arxiv.org/pdf/1301.3718.pdf)

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