├── .gitignore ├── Makefile ├── README.md ├── metadata ├── annotation.csv ├── config.yaml ├── flow_analysis.csv ├── guide_annotation.csv ├── merge_table.csv └── pipeline_config.yaml ├── requirements.txt └── src ├── CROP-mixingExperiments.R ├── analysis.py ├── assign_gRNA_cells.py ├── collect_expression.py ├── guides_to_ref.py ├── qc_plots.py └── screen_dynamics.py /.gitignore: -------------------------------------------------------------------------------- 1 | results/* 2 | *.png 3 | *.svg 4 | 5 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/README.md -------------------------------------------------------------------------------- /metadata/annotation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/metadata/annotation.csv -------------------------------------------------------------------------------- /metadata/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/metadata/config.yaml -------------------------------------------------------------------------------- /metadata/flow_analysis.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/metadata/flow_analysis.csv -------------------------------------------------------------------------------- /metadata/guide_annotation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/metadata/guide_annotation.csv -------------------------------------------------------------------------------- /metadata/merge_table.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/metadata/merge_table.csv -------------------------------------------------------------------------------- /metadata/pipeline_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/metadata/pipeline_config.yaml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/requirements.txt -------------------------------------------------------------------------------- /src/CROP-mixingExperiments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/src/CROP-mixingExperiments.R -------------------------------------------------------------------------------- /src/analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/src/analysis.py -------------------------------------------------------------------------------- /src/assign_gRNA_cells.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/src/assign_gRNA_cells.py -------------------------------------------------------------------------------- /src/collect_expression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/src/collect_expression.py -------------------------------------------------------------------------------- /src/guides_to_ref.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/src/guides_to_ref.py -------------------------------------------------------------------------------- /src/qc_plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/src/qc_plots.py -------------------------------------------------------------------------------- /src/screen_dynamics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epigen/crop-seq/HEAD/src/screen_dynamics.py --------------------------------------------------------------------------------