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1. transcriptome-dynamics-dmd-observability transcriptome-dynamics-dmd-observability Public

   Code to reproduce the Nature Communications manuscript "Learning perturbation-inducible cell states of novel compounds from observability analysis of transcriptome dynamics"

   Jupyter Notebook 4 2

2. KO_learning KO_learning Public

   ML models for learning Koopman operators and also Koopman generators.

   Jupyter Notebook

3. circuit-state circuit-state Public

   studying host-circuit phenotypes, host-circuit control, and circuit cell states

   Jupyter Notebook

4. process-RNAseq-fastq process-RNAseq-fastq Public

   shell scripts calling functions to process fastq files

   Shell

5. rna-tn-fusion rna-tn-fusion Public

   GNNs to integrate RNA-seq and Rb-TnSeq datasets

   Jupyter Notebook