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51,514 changes: 25,757 additions & 25,757 deletions DE_analysis/tables/de_stats_allExprs.csv
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4 changes: 2 additions & 2 deletions DE_analysis/tables/de_stats_fdr20_sorted.csv
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"","Length","gencodeID","ensemblID","gene_type","Symbol","EntrezID","Class","meanExprs","NumTx","gencodeTx","logFC","AveExpr","t","P.Value","adj.P.Val","B"
"ENSG00000269699.6",3066,"ENSG00000269699.6","ENSG00000269699","protein_coding","ZIM2",23619,"InGen",0.726190782334497,9,"ENST00000593711.6;ENST00000629319.2;ENST00000595671.5;ENST00000597281.5;ENST00000601070.5;ENST00000599935.5;ENST00000650111.1;ENST00000596270.1;ENST00000593931.1",-1.08601088522624,0.89702027931849,-5.52187889018213,2.07308409952771e-06,0.0553679301301861,3.39784116769199
"ENSG00000126368.6",2630,"ENSG00000126368.6","ENSG00000126368","protein_coding","NR1D1",9572,"InGen",10.3369710917094,1,"ENST00000246672.4",-0.767647739718869,4.61289572449009,-5.07069010840053,8.95610999268265e-06,0.119599892842284,3.35217294695315
"ENSG00000269699.6",3066,"ENSG00000269699.6","ENSG00000269699","protein_coding","ZIM2",23619,"InGen",0.726190782334497,9,"ENST00000593711.6;ENST00000629319.2;ENST00000595671.5;ENST00000597281.5;ENST00000601070.5;ENST00000599935.5;ENST00000650111.1;ENST00000596270.1;ENST00000593931.1",-1.08601088522624,0.89702027931849,-5.52187889018213,2.07308409952773e-06,0.0553679301301865,3.39784116769199
"ENSG00000126368.6",2630,"ENSG00000126368.6","ENSG00000126368","protein_coding","NR1D1",9572,"InGen",10.3369710917094,1,"ENST00000246672.4",-0.767647739718869,4.61289572449009,-5.07069010840053,8.95610999268259e-06,0.119599892842283,3.35217294695316
34 changes: 17 additions & 17 deletions bootcamp_intro.html
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28 changes: 14 additions & 14 deletions de_analysis.bib
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Expand Up @@ -48,23 +48,23 @@ @Article{colladotorres2017reproducible
url = {http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html},
}

@Manual{colladotorres2021jaffelab,
title = {jaffelab: Commonly used functions by the Jaffe lab},
author = {Leonardo Collado-Torres and Andrew E. Jaffe and Emily E. Burke},
year = {2021},
note = {R package version 0.99.32},
url = {https://github.com/LieberInstitute/jaffelab},
}

@Manual{colladotorres2023explore,
@Manual{colladotorres2024explore,
title = {Explore and download data from the recount project},
author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek},
year = {2023},
year = {2024},
url = {http://www.bioconductor.org/packages/recount},
note = {https://github.com/leekgroup/recount - R package version 1.16.1},
doi = {10.18129/B9.bioc.recount},
}

@Manual{colladotorres2024jaffelab,
title = {jaffelab: Commonly used functions by the Jaffe lab},
author = {Leonardo Collado-Torres and Andrew E. Jaffe and Emily E. Burke},
year = {2024},
note = {R package version 0.99.34},
url = {https://github.com/LieberInstitute/jaffelab},
}

@Article{ellis2018improving,
title = {Improving the value of public RNA-seq expression data by phenotype prediction},
author = {Shannon E. Ellis and Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
Expand All @@ -85,7 +85,7 @@ @Article{frazee2011recount

@Article{imada2020recounting,
title = {Recounting the FANTOM CAGE–Associated Transcriptome},
author = {Eddie-Luidy Imada and Diego Fernando Sanchez and Leonardo Collado-Torres and Christopher Wilks and Tejasvi Matam and Wikum Dinalankara and Aleksey Stupnikov and Francisco Lobo-Pereira and Chi-Wai Yip and Kayoko Yasuzawa and Naoto Kondo and Masayoshi Itoh and Harukazu Suzuki and Takeya Kasukawa and Chung Chau Hon and Michiel JL {de Hoon} and Jay W Shin and Piero Carninci and Andrew E. Jaffe and Jeffrey T. Leek and Alexander Favorov and Gl{\a'o}ria R Franco and Ben Langmead and Luigi Marchionni},
author = {Eddie-Luidy Imada and Diego Fernando Sanchez and Leonardo Collado-Torres and Christopher Wilks and Tejasvi Matam and Wikum Dinalankara and Aleksey Stupnikov and Francisco Lobo-Pereira and Chi-Wai Yip and Kayoko Yasuzawa and Naoto Kondo and Masayoshi Itoh and Harukazu Suzuki and Takeya Kasukawa and Chung Chau Hon and Michiel JL {de Hoon} and Jay W Shin and Piero Carninci and Andrew E. Jaffe and Jeffrey T. Leek and Alexander Favorov and Gl\'{o}ria R Franco and Ben Langmead and Luigi Marchionni},
year = {2020},
journal = {Genome Research},
doi = {10.1101/gr.254656.119},
Expand All @@ -112,14 +112,14 @@ @Article{mccarthy2012differential

@Manual{mller2020here,
title = {here: A Simpler Way to Find Your Files},
author = {Kirill M{\"u}ller},
author = {Kirill M\"{u}ller},
year = {2020},
note = {https://here.r-lib.org/, https://github.com/r-lib/here},
}

@Manual{morgan2020summarizedexperiment,
title = {SummarizedExperiment: SummarizedExperiment container},
author = {Martin Morgan and Valerie Obenchain and Jim Hester and Herv{\a'e} Pag{\a`e}s},
author = {Martin Morgan and Valerie Obenchain and Jim Hester and Herv\'{e} Pag\`{e}s},
year = {2020},
note = {R package version 1.20.0},
url = {https://bioconductor.org/packages/SummarizedExperiment},
Expand All @@ -134,7 +134,7 @@ @Manual{neuwirth2014rcolorbrewer

@Manual{ole2020biocstyle,
title = {BiocStyle: Standard styles for vignettes and other Bioconductor documents},
author = {Andrzej Ole{\a's} and Martin Morgan and Wolfgang Huber},
author = {Andrzej Ole\'{s} and Martin Morgan and Wolfgang Huber},
year = {2020},
note = {R package version 2.18.1},
url = {https://github.com/Bioconductor/BiocStyle},
Expand Down
43 changes: 23 additions & 20 deletions de_analysis_speaqeasy.html
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Expand Up @@ -1024,9 +1024,9 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
<li><em><a href="https://CRAN.R-project.org/package=devtools">devtools</a></em> (<a href='https://github.com/cboettig/knitcitations'>Boettiger, 2021</a>)</li>
<li><em><a href="https://bioconductor.org/packages/3.12/edgeR">edgeR</a></em></li>
<li><em><a href="https://CRAN.R-project.org/package=here">here</a></em> (<a href='http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html'>Collado-Torres, Nellore, Kammers, Ellis et al., 2017</a>)</li>
<li><em><a href="https://github.com/LieberInstitute/jaffelab">jaffelab</a></em> (<a href='https://github.com/LieberInstitute/jaffelab'>Collado-Torres, Jaffe, and Burke, 2021</a>)</li>
<li><em><a href="https://github.com/LieberInstitute/jaffelab">jaffelab</a></em> (<a href='http://www.bioconductor.org/packages/recount'>Collado-Torres, Nellore, Kammers, Ellis et al., 2024</a>)</li>
<li><em><a href="https://bioconductor.org/packages/3.12/limma">limma</a></em> (<a href='https://doi.org/10.1093/nar/gky102'>Ellis, Collado-Torres, Jaffe, and Leek, 2018</a>)</li>
<li><em><a href="https://CRAN.R-project.org/package=knitcitations">knitcitations</a></em> (<a href='http://www.bioconductor.org/packages/recount'>Collado-Torres, Nellore, Kammers, Ellis et al., 2023</a>)</li>
<li><em><a href="https://CRAN.R-project.org/package=knitcitations">knitcitations</a></em> (<a href='https://github.com/LieberInstitute/jaffelab'>Collado-Torres, Jaffe, and Burke, 2024</a>)</li>
<li><em><a href="https://bioconductor.org/packages/3.12/org.Hs.eg.db">org.Hs.eg.db</a></em> (<a href='https://doi.org/10.1186/1471-2105-12-449'>Frazee, Langmead, and Leek, 2011</a>)</li>
<li><em><a href="https://CRAN.R-project.org/package=pheatmap">pheatmap</a></em> (<a href='https://doi.org/10.1101/gr.254656.119'>Imada, Sanchez, Collado-Torres, Wilks et al., 2020</a>)</li>
<li><em><a href="https://CRAN.R-project.org/package=RColorBrewer">RColorBrewer</a></em> (<a href='https://doi.org/10.1093/nar/gks042'>McCarthy, Chen, and Smyth, 2012</a>)</li>
Expand All @@ -1041,9 +1041,9 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
<p>[2] C. Boettiger. <em>knitcitations: Citations for ‘Knitr’ Markdown Files</em>. R package version 1.0.12. 2021. &lt;URL:
<a href="https://github.com/cboettig/knitcitations" class="uri">https://github.com/cboettig/knitcitations</a>&gt;.</p>
<p>[3] L. Collado-Torres, A. E. Jaffe, and E. E. Burke. <em>jaffelab: Commonly used functions by the Jaffe lab</em>. R package
version 0.99.32. 2021. &lt;URL: <a href="https://github.com/LieberInstitute/jaffelab" class="uri">https://github.com/LieberInstitute/jaffelab</a>&gt;.</p>
version 0.99.34. 2024. &lt;URL: <a href="https://github.com/LieberInstitute/jaffelab" class="uri">https://github.com/LieberInstitute/jaffelab</a>&gt;.</p>
<p>[4] L. Collado-Torres, A. Nellore, K. Kammers, S. E. Ellis, et al. <em>Explore and download data from the recount
project</em>. <a href="https://github.com/leekgroup/recount" class="uri">https://github.com/leekgroup/recount</a> - R package version 1.16.1. 2023. DOI: 10.18129/B9.bioc.recount.
project</em>. <a href="https://github.com/leekgroup/recount" class="uri">https://github.com/leekgroup/recount</a> - R package version 1.16.1. 2024. DOI: 10.18129/B9.bioc.recount.
&lt;URL: <a href="http://www.bioconductor.org/packages/recount" class="uri">http://www.bioconductor.org/packages/recount</a>&gt;.</p>
<p>[5] L. Collado-Torres, A. Nellore, K. Kammers, S. E. Ellis, et al. “Reproducible RNA-seq analysis using recount2”.
In: <em>Nature Biotechnology</em> (2017). DOI: 10.1038/nbt.3838. &lt;URL:
Expand All @@ -1069,10 +1069,10 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
clusters”. In: <em>OMICS: A Journal of Integrative Biology</em> 16.5 (2012), pp. 284-287. DOI: 10.1089/omi.2011.0118.</p>
<pre class="r"><code># Time spent creating this report:
diff(c(timestart, Sys.time()))</code></pre>
<pre><code>## Time difference of 2.556757 mins</code></pre>
<pre><code>## Time difference of 1.790245 mins</code></pre>
<pre class="r"><code># Date this report was generated
message(Sys.time())</code></pre>
<pre><code>## 2023-07-14 13:53:30</code></pre>
<pre><code>## 2024-12-11 17:00:55</code></pre>
<pre class="r"><code># Reproducibility info
options(width = 120)
devtools::session_info()</code></pre>
Expand All @@ -1086,7 +1086,7 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2023-07-14
## date 2024-12-11
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date lib source
Expand All @@ -1095,7 +1095,7 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## assertthat 0.2.1 2019-03-21 [2] RSPM (R 4.0.3)
## backports 1.2.1 2020-12-09 [1] RSPM (R 4.0.3)
## base64enc 0.1-3 2015-07-28 [2] RSPM (R 4.0.3)
## bibtex 0.5.1 2023-07-14 [1] Github (ropensci/bibtex@eeb69da)
## bibtex 0.5.1 2024-12-11 [1] Github (ropensci/bibtex@12f8bef)
## Biobase * 2.50.0 2020-10-27 [1] Bioconductor
## BiocFileCache 1.14.0 2020-10-27 [1] Bioconductor
## BiocGenerics * 0.36.1 2021-04-16 [1] Bioconductor
Expand Down Expand Up @@ -1133,10 +1133,10 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## desc 1.2.0 2018-05-01 [2] RSPM (R 4.0.3)
## devtools * 2.3.2 2020-09-18 [2] RSPM (R 4.0.3)
## digest 0.6.27 2020-10-24 [2] RSPM (R 4.0.3)
## DO.db 2.9 2023-07-14 [1] Bioconductor
## DO.db 2.9 2024-12-11 [1] Bioconductor
## doRNG 1.8.2 2020-01-27 [1] RSPM (R 4.0.3)
## DOSE 3.16.0 2020-10-27 [1] Bioconductor
## downloader 0.4 2015-07-09 [1] RSPM (R 4.0.3)
## downloader 0.4 2015-07-09 [1] RSPM (R 4.0.5)
## dplyr 1.0.4 2021-02-02 [1] RSPM (R 4.0.3)
## DT 0.17 2021-01-06 [2] RSPM (R 4.0.3)
## edgeR * 3.32.1 2021-01-14 [1] Bioconductor
Expand All @@ -1154,7 +1154,7 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## fs 1.5.0 2020-07-31 [2] RSPM (R 4.0.3)
## generics 0.1.0 2020-10-31 [1] RSPM (R 4.0.3)
## GenomeInfoDb * 1.26.7 2021-04-08 [1] Bioconductor
## GenomeInfoDbData 1.2.4 2023-07-14 [1] Bioconductor
## GenomeInfoDbData 1.2.4 2024-12-11 [1] Bioconductor
## GenomicAlignments 1.26.0 2020-10-27 [1] Bioconductor
## GenomicFeatures 1.42.3 2021-04-01 [1] Bioconductor
## GenomicFiles 1.26.0 2020-10-27 [1] Bioconductor
Expand All @@ -1166,13 +1166,13 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## ggraph 2.0.4 2020-11-16 [1] RSPM (R 4.0.3)
## ggrepel 0.9.1 2021-01-15 [1] RSPM (R 4.0.3)
## glue 1.4.2 2020-08-27 [2] RSPM (R 4.0.3)
## GO.db 3.12.1 2023-07-14 [1] Bioconductor
## GO.db 3.12.1 2024-12-11 [1] Bioconductor
## googledrive 1.0.1 2020-05-05 [1] RSPM (R 4.0.0)
## GOSemSim 2.16.1 2020-10-29 [1] Bioconductor
## graphlayouts 0.7.1 2020-10-26 [1] RSPM (R 4.0.3)
## gridExtra 2.3 2017-09-09 [1] RSPM (R 4.0.3)
## gridExtra 2.3 2017-09-09 [1] RSPM (R 4.0.5)
## gtable 0.3.0 2019-03-25 [1] RSPM (R 4.0.3)
## here * 1.0.1 2020-12-13 [1] RSPM (R 4.0.3)
## here * 1.0.1 2020-12-13 [1] RSPM (R 4.0.5)
## highr 0.8 2019-03-20 [2] RSPM (R 4.0.3)
## Hmisc 4.4-2 2020-11-29 [1] RSPM (R 4.0.3)
## hms 1.0.0 2021-01-13 [1] RSPM (R 4.0.3)
Expand All @@ -1184,7 +1184,7 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## igraph 1.2.6 2020-10-06 [1] RSPM (R 4.0.3)
## IRanges * 2.24.1 2020-12-12 [1] Bioconductor
## iterators 1.0.13 2020-10-15 [1] RSPM (R 4.0.3)
## jaffelab * 0.99.32 2023-07-14 [1] Github (LieberInstitute/jaffelab@21e6574)
## jaffelab * 0.99.34 2024-12-11 [1] Github (LieberInstitute/jaffelab@a68c146)
## jpeg 0.1-8.1 2019-10-24 [1] RSPM (R 4.0.3)
## jquerylib 0.1.3 2020-12-17 [1] RSPM (R 4.0.3)
## jsonlite 1.7.2 2020-12-09 [2] RSPM (R 4.0.3)
Expand All @@ -1209,8 +1209,8 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## munsell 0.5.0 2018-06-12 [1] RSPM (R 4.0.3)
## nnet 7.3-15 2021-01-24 [3] RSPM (R 4.0.3)
## openssl 1.4.3 2020-09-18 [2] RSPM (R 4.0.3)
## org.Hs.eg.db * 3.12.0 2023-07-14 [1] Bioconductor
## pheatmap * 1.0.12 2019-01-04 [1] RSPM (R 4.0.3)
## org.Hs.eg.db * 3.12.0 2024-12-11 [1] Bioconductor
## pheatmap * 1.0.12 2019-01-04 [1] RSPM (R 4.0.5)
## pillar 1.4.7 2020-11-20 [2] RSPM (R 4.0.3)
## pkgbuild 1.2.0 2020-12-15 [2] RSPM (R 4.0.3)
## pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.0.3)
Expand All @@ -1226,6 +1226,9 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## ps 1.5.0 2020-12-05 [2] RSPM (R 4.0.3)
## purrr 0.3.4 2020-04-17 [2] RSPM (R 4.0.3)
## qvalue 2.22.0 2020-10-27 [1] Bioconductor
## R.methodsS3 1.8.1 2020-08-26 [1] RSPM (R 4.0.3)
## R.oo 1.24.0 2020-08-26 [1] RSPM (R 4.0.3)
## R.utils 2.10.1 2020-08-26 [1] RSPM (R 4.0.3)
## R6 2.5.0 2020-10-28 [2] RSPM (R 4.0.3)
## rafalib * 1.0.0 2015-08-09 [1] RSPM (R 4.0.0)
## rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.0.3)
Expand All @@ -1234,9 +1237,9 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## RCurl 1.98-1.2 2020-04-18 [1] RSPM (R 4.0.3)
## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.3)
## recount * 1.16.1 2020-12-18 [1] Bioconductor
## RefManageR 1.4.0 2023-07-14 [1] Github (ropensci/RefManageR@2409e32)
## RefManageR 1.4.3 2024-12-11 [1] Github (ropensci/RefManageR@d616da5)
## remotes 2.2.0 2020-07-21 [2] RSPM (R 4.0.3)
## rentrez 1.2.3 2020-11-10 [1] RSPM (R 4.0.3)
## rentrez 1.2.3 2020-11-10 [1] RSPM (R 4.0.5)
## reshape2 1.4.4 2020-04-09 [1] RSPM (R 4.0.3)
## rintrojs 0.2.2 2019-05-29 [1] RSPM (R 4.0.0)
## rlang 0.4.10 2020-12-30 [2] RSPM (R 4.0.3)
Expand Down Expand Up @@ -1279,7 +1282,7 @@ <h1><span class="header-section-number">2</span> Reproducibility</h1>
## xfun 0.21 2021-02-10 [2] RSPM (R 4.0.3)
## XML 3.99-0.5 2020-07-23 [1] RSPM (R 4.0.3)
## xml2 1.3.2 2020-04-23 [2] RSPM (R 4.0.3)
## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.0.3)
## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.0.5)
## XVector 0.30.0 2020-10-27 [1] Bioconductor
## yaml 2.2.1 2020-02-01 [2] RSPM (R 4.0.3)
## zlibbioc 1.36.0 2020-10-27 [1] Bioconductor
Expand Down
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