Imaging complements genomics in Fluidigm doublet detection

Please contact ([email protected] or [email protected] or [email protected]) if you have any questions or suggestions.

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Installation

Git clone a copy of code:

git clone https://github.com/GuanLab/Image_based_doublet_detection.git

Required dependencies

• python (3.6.5)
• matplotlib
• h5py
• imgaug
• ipython
• keras
• scikit-image
• tensorflow-gpu
• R(3.6.1)
• caret
• e1071
• pROC
• stringr
• perl (5.10.1)
• kallisto

Dataset

• images and transcript profiles
• trained models

Run prediction from saved model

bash example/run_prediction.sh

Run example

bash example/run_example.sh