├── 10X_Perturb_Code ├── 3prime.fa ├── GetMatrix.R ├── GetMatrix_Loop.R ├── GetPert_10X_2019.sh ├── ReadMe.md ├── fiveprime.fa ├── makeRef.sh ├── mapIt.sh └── temp.sh ├── CellComposition └── AdamsMethod.R ├── CodeDirectory_Current ├── BatchSample.v2.R ├── GetPerturbations.R ├── PertLM.R ├── PertLM_Mean.R ├── RunPipeline.sh ├── RunSTM.R ├── RunSTM.sh ├── RunSTM_clean.R ├── SharedVariable.R ├── TestGOTerms.R ├── TestWGNCA_eigen.R ├── TestWGNCA_eigen_mean.R ├── TestWGNCA_kruskal_eigen.v2.R ├── WGCNA.Get.Eigen.R ├── description.files.txt ├── load_Seurat.R └── niceDraw.R ├── CompareToHuman ├── ProcessSeurat_CI.R ├── ReadMe.md └── TestEnrichment.DE.R ├── DECode ├── RunLimma.R └── SumDE_Clean.R ├── DialoutCode ├── Perturb_mat_filt.py └── RunDialout.combine.sh ├── Dialout_Results └── GetPerturbations.R ├── README.md ├── SeuratObjects ├── GetData.n500.end.R └── GetData.n500.start.R ├── UpdatedSTM ├── GetModel.R └── MakeImages.R └── WGCNA_DE_Results ├── GetGenes.R └── TestWGCNA.R 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