├── .gitignore ├── mit2017 ├── pagoda2 │ ├── pbmc8k.Rmd │ ├── pbmc8k.nb.html │ └── tSNE.rds └── scde │ ├── chromaffin.Rmd │ ├── chromaffin.nb.html │ ├── pagoda.helpers.r │ ├── pagoda1.Rmd │ └── pagoda1.nb.html ├── nano2019 ├── walkthrough_nano.Rmd ├── walkthrough_nano.md └── walkthrough_nano_files │ └── figure-markdown_github │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-22-1.png │ ├── unnamed-chunk-23-1.png │ ├── unnamed-chunk-33-1.png │ ├── unnamed-chunk-36-1.png │ ├── unnamed-chunk-37-1.png │ ├── unnamed-chunk-38-1.png │ ├── unnamed-chunk-39-1.png │ ├── unnamed-chunk-40-1.png │ ├── unnamed-chunk-42-1.png │ ├── unnamed-chunk-43-1.png │ ├── unnamed-chunk-45-1.png │ ├── unnamed-chunk-46-1.png │ ├── unnamed-chunk-48-1.png │ ├── unnamed-chunk-50-1.png │ ├── unnamed-chunk-53-1.png │ ├── unnamed-chunk-56-1.png │ ├── unnamed-chunk-7-1.png │ ├── unnamed-chunk-8-1.png │ └── unnamed-chunk-9-1.png ├── scw2014 ├── setup.sh └── tutorials │ ├── WGCNA.Rmd │ ├── WGCNA.html │ ├── WGCNA.md │ ├── alignment.html │ ├── alignment.md │ ├── alignment.rmd │ ├── counts.RData │ ├── differential_expression.Rmd │ ├── differential_expression.html │ ├── differential_expression.md │ ├── figure │ ├── unnamed-chunk-10.png │ ├── unnamed-chunk-11.png │ ├── unnamed-chunk-12.png │ ├── unnamed-chunk-13.png │ ├── unnamed-chunk-14.png │ ├── unnamed-chunk-151.png │ ├── unnamed-chunk-152.png │ ├── unnamed-chunk-16.png │ ├── unnamed-chunk-17.png │ ├── unnamed-chunk-18.png │ ├── unnamed-chunk-19.png │ ├── unnamed-chunk-20.png │ ├── unnamed-chunk-21.png │ ├── unnamed-chunk-23.png │ ├── unnamed-chunk-251.png │ ├── unnamed-chunk-252.png │ ├── unnamed-chunk-4.png │ ├── unnamed-chunk-441.png │ ├── unnamed-chunk-442.png │ ├── unnamed-chunk-6.png │ ├── unnamed-chunk-7.png │ ├── unnamed-chunk-71.png │ ├── unnamed-chunk-72.png │ ├── unnamed-chunk-73.png │ ├── unnamed-chunk-74.png │ └── unnamed-chunk-9.png │ ├── mode.fail.dist.RData │ ├── module_black.txt │ ├── module_blue.txt │ ├── module_brown.txt │ ├── module_green.txt │ ├── module_pink.txt │ ├── module_red.txt │ ├── module_turquoise.txt │ ├── module_yellow.txt │ ├── monocle_tutorial_oedsymbol.Rmd │ ├── monocle_tutorial_oedsymbol.html │ ├── monocle_tutorial_oedsymbol.md │ ├── oed.RData │ ├── oed_win.RData │ ├── subpop_tutorial.Rmd │ ├── subpop_tutorial.html │ └── subpop_tutorial.md ├── scw2015 ├── README.md ├── alignment │ ├── alignment-markdown-precursor.md │ ├── counts.sh │ └── setup_alignment.sh ├── differential_expression │ ├── ES_MEF_raw.RData │ ├── differential_expression.Rmd │ └── gene_name_map.RData ├── required_libraries.txt ├── setup.sh ├── subpopulations │ └── analysis_of_heterogeneity_and_subpopulations.Rmd └── wgcna │ └── WGCNA.Rmd └── scw2016 ├── README.md ├── data ├── README.md ├── cd.RData ├── fpm.RData ├── go.env.RData ├── knn.RData ├── pwpca.RData ├── sg.RData └── varinfo.RData ├── required_libraries.txt ├── setup.sh └── tutorials ├── alignment └── alignment.md ├── batcheffects ├── Hicks.Rmd ├── Hicks.html └── figures │ ├── .DS_Store │ ├── fastq.png │ ├── fastqfile.png │ ├── hicks-problemsbatch.jpeg │ ├── leek-batcheffects.png │ ├── tung-recommended-studydesign.png │ ├── tung-studydesign.png │ └── wildwest.png ├── heterogeneity ├── .Rproj.user │ └── BF0E4747 │ │ └── sdb │ │ └── prop │ │ ├── 7A4B1340 │ │ ├── 9E120CB9 │ │ ├── E646A55E │ │ └── INDEX ├── figure-2016 │ ├── monocle-2-1.png │ ├── monocle-2-2.png │ ├── monocle-2-3.png │ ├── pagoda-marker-1.png │ ├── pagoda-marker-2.png │ ├── pagoda-tam-1.png │ ├── pagoda-tsne-1.png │ ├── pca-1.png │ ├── scde-1.png │ ├── scde-2-1.png │ ├── scde-2-2.png │ ├── tsne-1.png │ └── tsne-2-1.png ├── heterogeneity.Rmd ├── heterogeneity.Rproj ├── heterogeneity.html └── heterogeneity.md └── wgcna ├── WGCNA.html ├── WGCNA.md ├── figure-2016 ├── expression-pattern-1.png ├── module-detection-1.png ├── module-detection-2.png ├── module-detection-3.png └── softpower 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