├── .gitignore ├── .gitmodules ├── README.md ├── TEdetectEval.R ├── dataInfo.csv ├── figures.R ├── general.R ├── helper_scripts ├── alignToFasta.sh ├── align_parser.py ├── align_to_out.py ├── generateDict.py ├── getRandomSeq.py └── pylibs │ ├── __pycache__ │ └── fileparser.cpython-37.pyc │ └── fileparser.py ├── libs ├── countTableHandler.R ├── dataProcessing.X ├── deseq2.R ├── func.R ├── generateExprAnaTab.R ├── loadSalmonTE.R ├── loadSimulation.R ├── loadSquire.R ├── loadTEtools.R ├── loadTEtranscripts.R ├── loadTelescope.R └── styling.R ├── run.sh ├── sampleTEs.R ├── simulation_polyester.R └── tables.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Hoffmann-Lab/TEdetectionEvaluation/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 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