├── .DS_Store ├── Experiments ├── .DS_Store ├── FetalLiverExperiment │ ├── MI.R │ ├── data │ │ └── unzip.sh │ ├── gene_relevance.R │ ├── grnboost2.py │ ├── instruction.txt │ ├── plot_LE_dim.py │ ├── plot_reduce_sample_experiment.py │ ├── plot_zv_recon_scale.py │ ├── prepare_input_for_grn.py │ ├── repo_FetalLiver_1_preprocess.py │ ├── repo_FetalLiver_2_SetupInput.py │ ├── repo_FetalLiver_3_model.py │ ├── repo_FetalLiver_4_analysis.py │ ├── repo_FetalLiver_5_sampling.py │ └── run_FetalLiver.sh ├── Imaging │ ├── GeneRelevanceVisualization.py │ ├── gene_relevance.R │ ├── load_MNIST.py │ ├── run_MNIST.py │ ├── run_MNIST.sh │ └── run_MNIST_subset.py ├── TimeExperiment │ ├── instruction.txt │ ├── load_data.py │ ├── preprocessing_10X.py │ ├── preprocessing_SNARESeq.R │ ├── run_experiment.sh │ └── run_siVAE.py ├── graph_comparison │ ├── circos.R │ ├── generate_run_list.py │ ├── graph_analysis.py │ ├── iPSC_neuronal │ │ ├── check_rita.R │ │ ├── check_rita.py │ │ ├── get_data.sh │ │ ├── mv_rita_data.sh │ │ ├── plot_batch.py │ │ ├── preprocess_D11.py │ │ ├── preprocess_D52.py │ │ ├── rda2h5ad.R │ │ ├── run.sh │ │ ├── vcf │ │ │ ├── burden_test.py │ │ │ ├── download_fastq.sh │ │ │ ├── download_vcf.py │ │ │ ├── download_vcf.sh │ │ │ ├── filter_MT.py │ │ │ └── vcf_ftp_list.txt │ │ └── wgs_metadata.py │ └── run_siVAE.py ├── instructions.txt ├── scvi │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ ├── _compat.cpython-36.pyc │ │ ├── _constants.cpython-36.pyc │ │ ├── _docs.cpython-36.pyc │ │ ├── _settings.cpython-36.pyc │ │ └── _utils.cpython-36.pyc │ ├── _compat.py │ ├── _constants.py │ ├── _docs.py │ ├── _settings.py │ ├── _utils.py │ ├── core │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ ├── _log_likelihood.cpython-36.pyc │ │ │ └── _metrics.cpython-36.pyc │ │ ├── _log_likelihood.py │ │ ├── _metrics.py │ │ ├── data_loaders │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ ├── annotation_data_loader.cpython-36.pyc │ │ │ │ ├── scvi_data_loader.cpython-36.pyc │ │ │ │ └── total_data_loader.cpython-36.pyc │ │ │ ├── annotation_data_loader.py │ │ │ ├── scvi_data_loader.py │ │ │ └── total_data_loader.py │ │ ├── distributions │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ └── _negative_binomial.cpython-36.pyc │ │ │ └── _negative_binomial.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ ├── _utils.cpython-36.pyc │ │ │ │ ├── archesmixin.cpython-36.pyc │ │ │ │ ├── base.cpython-36.pyc │ │ │ │ ├── rnamixin.cpython-36.pyc │ │ │ │ └── vaemixin.cpython-36.pyc │ │ │ ├── _utils.py │ │ │ ├── archesmixin.py │ │ │ ├── base.py │ │ │ ├── rnamixin.py │ │ │ └── vaemixin.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ ├── autozivae.cpython-36.pyc │ │ │ │ ├── classifier.cpython-36.pyc │ │ │ │ ├── jvae.cpython-36.pyc │ │ │ │ ├── scanvae.cpython-36.pyc │ │ │ │ ├── totalvae.cpython-36.pyc │ │ │ │ ├── utils.cpython-36.pyc │ │ │ │ ├── vae.cpython-36.pyc │ │ │ │ └── vaec.cpython-36.pyc │ │ │ ├── _base │ │ │ │ ├── __init__.py │ │ │ │ └── __pycache__ │ │ │ │ │ └── __init__.cpython-36.pyc │ │ │ ├── autozivae.py │ │ │ ├── classifier.py │ │ │ ├── jvae.py │ │ │ ├── scanvae.py │ │ │ ├── totalvae.py │ │ │ ├── utils.py │ │ │ ├── vae.py │ │ │ └── vaec.py │ │ ├── trainers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ ├── annotation.cpython-36.pyc │ │ │ │ ├── inference.cpython-36.pyc │ │ │ │ ├── jvae_trainer.cpython-36.pyc │ │ │ │ ├── total_inference.cpython-36.pyc │ │ │ │ └── trainer.cpython-36.pyc │ │ │ ├── annotation.py │ │ │ ├── inference.py │ │ │ ├── jvae_trainer.py │ │ │ ├── total_inference.py │ │ │ └── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ └── differential.cpython-36.pyc │ │ │ └── differential.py │ ├── data │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ ├── _anndata.cpython-36.pyc │ │ │ ├── _datasets.cpython-36.pyc │ │ │ ├── _preprocessing.cpython-36.pyc │ │ │ ├── _scvidataset.cpython-36.pyc │ │ │ ├── _utils._check_is_counts-107.py36m.1.nbc │ │ │ ├── _utils._check_is_counts-107.py36m.nbi │ │ │ └── _utils.cpython-36.pyc │ │ ├── _anndata.py │ │ ├── _built_in_data │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ ├── _brain_large.cpython-36.pyc │ │ │ │ ├── _cite_seq.cpython-36.pyc │ │ │ │ ├── _cortex.cpython-36.pyc │ │ │ │ ├── _csv.cpython-36.pyc │ │ │ │ ├── _dataset_10x.cpython-36.pyc │ │ │ │ ├── _download.cpython-36.pyc │ │ │ │ ├── _loom.cpython-36.pyc │ │ │ │ ├── _pbmc.cpython-36.pyc │ │ │ │ ├── _seqfish.cpython-36.pyc │ │ │ │ ├── _smfish.cpython-36.pyc │ │ │ │ └── _synthetic.cpython-36.pyc │ │ │ ├── _brain_large.py │ │ │ ├── _cite_seq.py │ │ │ ├── _cortex.py │ │ │ ├── _csv.py │ │ │ ├── _dataset_10x.py │ │ │ ├── _download.py │ │ │ ├── _loom.py │ │ │ ├── _pbmc.py │ │ │ ├── _seqfish.py │ │ │ ├── _smfish.py │ │ │ └── _synthetic.py │ │ ├── _datasets.py │ │ ├── _preprocessing.py │ │ ├── _scvidataset.py │ │ └── _utils.py │ └── model │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ ├── _utils.cpython-36.pyc │ │ ├── autozi.cpython-36.pyc │ │ ├── gimvi.cpython-36.pyc │ │ ├── linear_scvi.cpython-36.pyc │ │ ├── scanvi.cpython-36.pyc │ │ ├── scvi.cpython-36.pyc │ │ └── totalvi.cpython-36.pyc │ │ ├── _utils.py │ │ ├── autozi.py │ │ ├── gimvi.py │ │ ├── linear_scvi.py │ │ ├── scanvi.py │ │ ├── scvi.py │ │ └── totalvi.py └── simluation │ └── simulate_GRN │ ├── 210804_Figure1 │ └── simulate.py │ ├── adj_to_cov.R │ ├── adjacency.py │ ├── analyze_runs.py │ ├── exp211013 │ ├── distributions.py │ ├── nonlinear.py │ └── plots.py │ ├── network_class.py │ ├── run.py │ ├── run.sh │ └── run_analyze.sh ├── LICENSE.txt ├── README.md ├── deepexplain ├── __init__.py ├── tensorflow │ ├── __init__.py │ ├── methods.py │ └── utils.py └── tests │ ├── __init__.py │ └── test_tensorflow.py ├── sample_fetal_liver_atlas_dataset.h5ad ├── setup.cfg ├── setup.py ├── siVAE ├── FeatureImportance.py ├── __init__.py ├── classifier.py ├── data │ ├── __init__.py │ ├── data_handler.py │ ├── tfdata.py │ └── tfrecord.py ├── gsea.py ├── model │ ├── VAE.py │ ├── __init__.py │ ├── analysis.py │ ├── layer.py │ ├── output │ │ ├── analysis.py │ │ ├── degree_centrality.py │ │ ├── geneset_annotation.py │ │ ├── neighborhood.py │ │ ├── output_handler.py │ │ └── plot.py │ ├── plot.py │ ├── regressor.py │ ├── siVAE.py │ └── util.py ├── plot_gmm.py ├── run_model.py └── util.py ├── tensorflow_forward_ad ├── .style.yapf ├── BUILD ├── __init__.py ├── bfs.py ├── bfs_tests.py ├── cbfs.c ├── cbfs.pyx ├── fwgrad.py ├── fwgrad_tests.py ├── graph.py ├── logger.py ├── maxpool_gradgrad.py ├── maxpool_gradgrad_tests.py ├── second_order.py ├── second_order_tests.py └── setup_cbfs.py └── tutorial ├── output_20_0.svg ├── output_21_0.svg ├── output_22_0.svg ├── output_24_0.svg ├── output_26_0.png ├── output_27_0.png ├── output_30_1.png ├── output_32_0.png ├── output_41_0.svg └── tutorial.md /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/.DS_Store -------------------------------------------------------------------------------- /Experiments/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/.DS_Store -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/MI.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/MI.R -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/data/unzip.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/data/unzip.sh -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/gene_relevance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/gene_relevance.R -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/grnboost2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/grnboost2.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/instruction.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/instruction.txt -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/plot_LE_dim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/plot_LE_dim.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/plot_reduce_sample_experiment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/plot_reduce_sample_experiment.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/plot_zv_recon_scale.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/plot_zv_recon_scale.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/prepare_input_for_grn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/prepare_input_for_grn.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/repo_FetalLiver_1_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/repo_FetalLiver_1_preprocess.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/repo_FetalLiver_2_SetupInput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/repo_FetalLiver_2_SetupInput.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/repo_FetalLiver_3_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/repo_FetalLiver_3_model.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/repo_FetalLiver_4_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/repo_FetalLiver_4_analysis.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/repo_FetalLiver_5_sampling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/repo_FetalLiver_5_sampling.py -------------------------------------------------------------------------------- /Experiments/FetalLiverExperiment/run_FetalLiver.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/FetalLiverExperiment/run_FetalLiver.sh -------------------------------------------------------------------------------- /Experiments/Imaging/GeneRelevanceVisualization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/Imaging/GeneRelevanceVisualization.py -------------------------------------------------------------------------------- /Experiments/Imaging/gene_relevance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/Imaging/gene_relevance.R -------------------------------------------------------------------------------- /Experiments/Imaging/load_MNIST.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/Imaging/load_MNIST.py -------------------------------------------------------------------------------- /Experiments/Imaging/run_MNIST.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/Imaging/run_MNIST.py -------------------------------------------------------------------------------- /Experiments/Imaging/run_MNIST.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/Imaging/run_MNIST.sh -------------------------------------------------------------------------------- /Experiments/Imaging/run_MNIST_subset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/Imaging/run_MNIST_subset.py -------------------------------------------------------------------------------- /Experiments/TimeExperiment/instruction.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/TimeExperiment/instruction.txt -------------------------------------------------------------------------------- /Experiments/TimeExperiment/load_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/TimeExperiment/load_data.py -------------------------------------------------------------------------------- /Experiments/TimeExperiment/preprocessing_10X.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/TimeExperiment/preprocessing_10X.py -------------------------------------------------------------------------------- /Experiments/TimeExperiment/preprocessing_SNARESeq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/TimeExperiment/preprocessing_SNARESeq.R -------------------------------------------------------------------------------- /Experiments/TimeExperiment/run_experiment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/TimeExperiment/run_experiment.sh -------------------------------------------------------------------------------- /Experiments/TimeExperiment/run_siVAE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/TimeExperiment/run_siVAE.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/circos.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/circos.R -------------------------------------------------------------------------------- /Experiments/graph_comparison/generate_run_list.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/generate_run_list.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/graph_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/graph_analysis.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/check_rita.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/check_rita.R -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/check_rita.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/check_rita.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/get_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/get_data.sh -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/mv_rita_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/mv_rita_data.sh -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/plot_batch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/plot_batch.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/preprocess_D11.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/preprocess_D11.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/preprocess_D52.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/preprocess_D52.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/rda2h5ad.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/rda2h5ad.R -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/run.sh -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/vcf/burden_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/vcf/burden_test.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/vcf/download_fastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/vcf/download_fastq.sh -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/vcf/download_vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/vcf/download_vcf.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/vcf/download_vcf.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/vcf/download_vcf.sh -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/vcf/filter_MT.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/vcf/filter_MT.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/vcf/vcf_ftp_list.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Experiments/graph_comparison/iPSC_neuronal/wgs_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/iPSC_neuronal/wgs_metadata.py -------------------------------------------------------------------------------- /Experiments/graph_comparison/run_siVAE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/graph_comparison/run_siVAE.py -------------------------------------------------------------------------------- /Experiments/instructions.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/instructions.txt -------------------------------------------------------------------------------- /Experiments/scvi/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/__pycache__/_compat.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/__pycache__/_compat.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/__pycache__/_constants.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/__pycache__/_constants.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/__pycache__/_docs.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/__pycache__/_docs.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/__pycache__/_settings.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/__pycache__/_settings.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/__pycache__/_utils.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/__pycache__/_utils.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/_compat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/_compat.py -------------------------------------------------------------------------------- /Experiments/scvi/_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/_constants.py -------------------------------------------------------------------------------- /Experiments/scvi/_docs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/_docs.py -------------------------------------------------------------------------------- /Experiments/scvi/_settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/_settings.py -------------------------------------------------------------------------------- /Experiments/scvi/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/_utils.py -------------------------------------------------------------------------------- /Experiments/scvi/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/__pycache__/_log_likelihood.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/__pycache__/_log_likelihood.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/__pycache__/_metrics.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/__pycache__/_metrics.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/_log_likelihood.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/_log_likelihood.py -------------------------------------------------------------------------------- /Experiments/scvi/core/_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/_metrics.py -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/__pycache__/annotation_data_loader.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/__pycache__/annotation_data_loader.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/__pycache__/scvi_data_loader.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/__pycache__/scvi_data_loader.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/__pycache__/total_data_loader.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/__pycache__/total_data_loader.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/annotation_data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/annotation_data_loader.py -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/scvi_data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/scvi_data_loader.py -------------------------------------------------------------------------------- /Experiments/scvi/core/data_loaders/total_data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/data_loaders/total_data_loader.py -------------------------------------------------------------------------------- /Experiments/scvi/core/distributions/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/distributions/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/distributions/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/distributions/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/distributions/__pycache__/_negative_binomial.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/distributions/__pycache__/_negative_binomial.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/distributions/_negative_binomial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/distributions/_negative_binomial.py -------------------------------------------------------------------------------- /Experiments/scvi/core/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/models/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/models/__pycache__/_utils.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/__pycache__/_utils.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/models/__pycache__/archesmixin.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/__pycache__/archesmixin.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/models/__pycache__/base.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/__pycache__/base.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/models/__pycache__/rnamixin.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/__pycache__/rnamixin.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/models/__pycache__/vaemixin.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/__pycache__/vaemixin.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/models/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/_utils.py -------------------------------------------------------------------------------- /Experiments/scvi/core/models/archesmixin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/archesmixin.py -------------------------------------------------------------------------------- /Experiments/scvi/core/models/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/base.py -------------------------------------------------------------------------------- /Experiments/scvi/core/models/rnamixin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/rnamixin.py -------------------------------------------------------------------------------- /Experiments/scvi/core/models/vaemixin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/models/vaemixin.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/autozivae.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/autozivae.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/classifier.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/classifier.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/jvae.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/jvae.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/scanvae.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/scanvae.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/totalvae.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/totalvae.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/utils.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/utils.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/vae.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/vae.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/__pycache__/vaec.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/__pycache__/vaec.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/_base/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/_base/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/_base/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/_base/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/autozivae.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/autozivae.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/classifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/classifier.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/jvae.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/jvae.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/scanvae.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/scanvae.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/totalvae.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/totalvae.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/utils.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/vae.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/vae.py -------------------------------------------------------------------------------- /Experiments/scvi/core/modules/vaec.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/modules/vaec.py -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/__pycache__/annotation.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/__pycache__/annotation.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/__pycache__/inference.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/__pycache__/inference.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/__pycache__/jvae_trainer.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/__pycache__/jvae_trainer.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/__pycache__/total_inference.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/__pycache__/total_inference.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/__pycache__/trainer.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/__pycache__/trainer.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/annotation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/annotation.py -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/inference.py -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/jvae_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/jvae_trainer.py -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/total_inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/total_inference.py -------------------------------------------------------------------------------- /Experiments/scvi/core/trainers/trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/trainers/trainer.py -------------------------------------------------------------------------------- /Experiments/scvi/core/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/utils/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/core/utils/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/utils/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/utils/__pycache__/differential.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/utils/__pycache__/differential.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/core/utils/differential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/core/utils/differential.py -------------------------------------------------------------------------------- /Experiments/scvi/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/_anndata.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/_anndata.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/_datasets.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/_datasets.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/_preprocessing.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/_preprocessing.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/_scvidataset.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/_scvidataset.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/_utils._check_is_counts-107.py36m.1.nbc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/_utils._check_is_counts-107.py36m.1.nbc -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/_utils._check_is_counts-107.py36m.nbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/_utils._check_is_counts-107.py36m.nbi -------------------------------------------------------------------------------- /Experiments/scvi/data/__pycache__/_utils.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/__pycache__/_utils.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_anndata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_anndata.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_brain_large.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_brain_large.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_cite_seq.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_cite_seq.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_cortex.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_cortex.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_csv.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_csv.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_dataset_10x.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_dataset_10x.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_download.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_download.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_loom.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_loom.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_pbmc.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_pbmc.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_seqfish.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_seqfish.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_smfish.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_smfish.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/__pycache__/_synthetic.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/__pycache__/_synthetic.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_brain_large.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_brain_large.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_cite_seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_cite_seq.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_cortex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_cortex.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_csv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_csv.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_dataset_10x.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_dataset_10x.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_download.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_loom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_loom.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_pbmc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_pbmc.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_seqfish.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_seqfish.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_smfish.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_smfish.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_built_in_data/_synthetic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_built_in_data/_synthetic.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_datasets.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_preprocessing.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_scvidataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_scvidataset.py -------------------------------------------------------------------------------- /Experiments/scvi/data/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/data/_utils.py -------------------------------------------------------------------------------- /Experiments/scvi/model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__init__.py -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/_utils.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/_utils.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/autozi.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/autozi.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/gimvi.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/gimvi.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/linear_scvi.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/linear_scvi.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/scanvi.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/scanvi.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/scvi.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/scvi.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/__pycache__/totalvi.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/__pycache__/totalvi.cpython-36.pyc -------------------------------------------------------------------------------- /Experiments/scvi/model/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/_utils.py -------------------------------------------------------------------------------- /Experiments/scvi/model/autozi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/autozi.py -------------------------------------------------------------------------------- /Experiments/scvi/model/gimvi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/gimvi.py -------------------------------------------------------------------------------- /Experiments/scvi/model/linear_scvi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/linear_scvi.py -------------------------------------------------------------------------------- /Experiments/scvi/model/scanvi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/scanvi.py -------------------------------------------------------------------------------- /Experiments/scvi/model/scvi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/scvi.py -------------------------------------------------------------------------------- /Experiments/scvi/model/totalvi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/scvi/model/totalvi.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/210804_Figure1/simulate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/210804_Figure1/simulate.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/adj_to_cov.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/adj_to_cov.R -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/adjacency.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/adjacency.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/analyze_runs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/analyze_runs.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/exp211013/distributions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/exp211013/distributions.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/exp211013/nonlinear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/exp211013/nonlinear.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/exp211013/plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/exp211013/plots.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/network_class.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/network_class.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/run.py -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/run.sh -------------------------------------------------------------------------------- /Experiments/simluation/simulate_GRN/run_analyze.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/Experiments/simluation/simulate_GRN/run_analyze.sh -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/README.md -------------------------------------------------------------------------------- /deepexplain/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /deepexplain/tensorflow/__init__.py: -------------------------------------------------------------------------------- 1 | from .methods import DeepExplain -------------------------------------------------------------------------------- /deepexplain/tensorflow/methods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/deepexplain/tensorflow/methods.py -------------------------------------------------------------------------------- /deepexplain/tensorflow/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/deepexplain/tensorflow/utils.py -------------------------------------------------------------------------------- /deepexplain/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /deepexplain/tests/test_tensorflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/deepexplain/tests/test_tensorflow.py -------------------------------------------------------------------------------- /sample_fetal_liver_atlas_dataset.h5ad: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/sample_fetal_liver_atlas_dataset.h5ad -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | description-file = README.md 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/setup.py -------------------------------------------------------------------------------- /siVAE/FeatureImportance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/FeatureImportance.py -------------------------------------------------------------------------------- /siVAE/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/__init__.py -------------------------------------------------------------------------------- /siVAE/classifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/classifier.py -------------------------------------------------------------------------------- /siVAE/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/data/__init__.py -------------------------------------------------------------------------------- /siVAE/data/data_handler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/data/data_handler.py -------------------------------------------------------------------------------- /siVAE/data/tfdata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/data/tfdata.py -------------------------------------------------------------------------------- /siVAE/data/tfrecord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/data/tfrecord.py -------------------------------------------------------------------------------- /siVAE/gsea.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/gsea.py -------------------------------------------------------------------------------- /siVAE/model/VAE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/VAE.py -------------------------------------------------------------------------------- /siVAE/model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/__init__.py -------------------------------------------------------------------------------- /siVAE/model/analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/analysis.py -------------------------------------------------------------------------------- /siVAE/model/layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/layer.py -------------------------------------------------------------------------------- /siVAE/model/output/analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/output/analysis.py -------------------------------------------------------------------------------- /siVAE/model/output/degree_centrality.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/output/degree_centrality.py -------------------------------------------------------------------------------- /siVAE/model/output/geneset_annotation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/output/geneset_annotation.py -------------------------------------------------------------------------------- /siVAE/model/output/neighborhood.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/output/neighborhood.py -------------------------------------------------------------------------------- /siVAE/model/output/output_handler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/output/output_handler.py -------------------------------------------------------------------------------- /siVAE/model/output/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/output/plot.py -------------------------------------------------------------------------------- /siVAE/model/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/plot.py -------------------------------------------------------------------------------- /siVAE/model/regressor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/regressor.py -------------------------------------------------------------------------------- /siVAE/model/siVAE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/siVAE.py -------------------------------------------------------------------------------- /siVAE/model/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/model/util.py -------------------------------------------------------------------------------- /siVAE/plot_gmm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/plot_gmm.py -------------------------------------------------------------------------------- /siVAE/run_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/run_model.py -------------------------------------------------------------------------------- /siVAE/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/siVAE/util.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/.style.yapf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/.style.yapf -------------------------------------------------------------------------------- /tensorflow_forward_ad/BUILD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/BUILD -------------------------------------------------------------------------------- /tensorflow_forward_ad/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/__init__.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/bfs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/bfs.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/bfs_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/bfs_tests.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/cbfs.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/cbfs.c -------------------------------------------------------------------------------- /tensorflow_forward_ad/cbfs.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/cbfs.pyx -------------------------------------------------------------------------------- /tensorflow_forward_ad/fwgrad.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/fwgrad.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/fwgrad_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/fwgrad_tests.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/graph.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/logger.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/maxpool_gradgrad.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/maxpool_gradgrad.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/maxpool_gradgrad_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/maxpool_gradgrad_tests.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/second_order.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/second_order.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/second_order_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/second_order_tests.py -------------------------------------------------------------------------------- /tensorflow_forward_ad/setup_cbfs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tensorflow_forward_ad/setup_cbfs.py -------------------------------------------------------------------------------- /tutorial/output_20_0.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_20_0.svg -------------------------------------------------------------------------------- /tutorial/output_21_0.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_21_0.svg -------------------------------------------------------------------------------- /tutorial/output_22_0.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_22_0.svg -------------------------------------------------------------------------------- /tutorial/output_24_0.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_24_0.svg -------------------------------------------------------------------------------- /tutorial/output_26_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_26_0.png -------------------------------------------------------------------------------- /tutorial/output_27_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_27_0.png -------------------------------------------------------------------------------- /tutorial/output_30_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_30_1.png -------------------------------------------------------------------------------- /tutorial/output_32_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_32_0.png -------------------------------------------------------------------------------- /tutorial/output_41_0.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/output_41_0.svg -------------------------------------------------------------------------------- /tutorial/tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quon-titative-biology/siVAE/HEAD/tutorial/tutorial.md --------------------------------------------------------------------------------