├── .gitignore ├── README.md ├── manuscript ├── Makefile ├── betternorm.tex ├── bmc-mathphys.bst ├── bmcart-biblio.sty ├── bmcart.cls ├── comments.Rmd ├── pics │ ├── deconvolution.svg │ ├── figure_deconv_sim.tex │ ├── figure_existing_sim.tex │ ├── figure_realdata.tex │ ├── figure_zerosim.tex │ ├── library_ring.svg │ └── zero_effect.R ├── references.bib └── suppmat.tex ├── realdata ├── DESeq2.R ├── GOAnalysis.R ├── HVGAnalysis.R ├── Klein.R ├── Kowalczyk.R ├── Macosko.R ├── Zeisel.R ├── edgeR.R ├── functions.R ├── plotKleinParam.R └── switchTestedgeR.R └── simulations ├── brittlesim.R ├── complexity.R ├── fewcounts.R ├── highcounts.R ├── lowcounts.R ├── poolsim.R ├── poolsim.Rout.save ├── results ├── robustsim.R ├── saturated.sh ├── standerr.R ├── standerr.Rout.save ├── weightsim.R └── weightsim.Rout.save /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MarioniLab/Deconvolution2016/HEAD/.gitignore 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