├── .gitignore ├── README.md └── SRC ├── ComBVAE ├── CVAE_model.py ├── CVAE_multilableClas_model.py ├── ComputeLogFCOfPredictionsAll.py ├── DenoisingAE_model.py ├── DenoisingAE_multilableClas_model.py ├── GenerateCells.py ├── InspectReconstruction.py ├── README.txt ├── RunModels.py ├── Training.py ├── Utils.py ├── libraries.py └── logger.py ├── ManuscriptFigures ├── 00_LPSPlusMinusAnalysis.ipynb ├── Conf.R ├── Figure1_CDEFGH.ipynb ├── Figure1_I-GeneLevel.ipynb ├── Figure2_ABC.ipynb ├── Figure2_D.ipynb ├── Figure3_A.ipynb ├── Figure3_B.ipynb ├── Figure3_CD.ipynb ├── Figure3_E.ipynb ├── Figure3_F.ipynb ├── Figure4_A.ipynb ├── Figure4_BCEFHI.ipynb ├── Figure4_BEH.ipynb ├── Figure5_C.ipynb ├── Figure5_DE.ipynb ├── Figure5_F.ipynb ├── Figure5_G.ipynb ├── Main.R ├── SuppFigure1_F.ipynb ├── SuppFigure1_G.ipynb ├── SuppFigure1_HZ.ipynb ├── SuppFigure_2AB.ipynb ├── SuppFigure_2Z.ipynb ├── SuppFigure_5CD.ipynb ├── SuppFigure_5E.ipynb ├── Utilities.R ├── libraries.py └── parameters.py └── Pipeline ├── 08_filterGenesGuides.py ├── 09_TestControlGuidesRegression.py ├── 09_TestKOGuidesRegression.py ├── 11_reduceGuidesToTargetGenes.py ├── 13_TestTargetGenes.py ├── Notebooks ├── 01-upstream-qc.ipynb ├── 02-downstream-qc.ipynb ├── 03-mergeWithHash.ipynb ├── 04-mergeWithCrispr.ipynb ├── 05-downstreamIntegration.ipynb ├── 06-scoreGenesets.ipynb ├── 07-inferDepletedGuides.ipynb ├── 08_SelectCellsAfterEM.ipynb ├── 10_selectKOGuides.ipynb ├── 12_selectSignificantlyPerturbedCells.ipynb ├── 14_GenerateGeneAndKOModules.ipynb ├── Conf.R ├── Main.R ├── RunNBMixedEffectLinearReg.sh ├── Utilities.R ├── libraries.py └── parameters.py ├── libraries.py └── parameters.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EraslanBas/PerturbDecode/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: 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