.gitignore
.travis.yml
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
version.py
MICA/__init__.py
MICA/mica.py
MICA/mica_ge.py
MICA/mica_mds.py
MICA/mica_pca.py
MICA/mica_umap.py
MICA.egg-info/PKG-INFO
MICA.egg-info/SOURCES.txt
MICA.egg-info/dependency_links.txt
MICA.egg-info/entry_points.txt
MICA.egg-info/requires.txt
MICA.egg-info/top_level.txt
MICA/analysis/__init__.py
MICA/analysis/evaluation/__init__.py
MICA/analysis/evaluation/clustering_performance/ID_conversion.R
MICA/analysis/evaluation/clustering_performance/__init__.py
MICA/analysis/evaluation/clustering_performance/eval.py
MICA/analysis/evaluation/clustering_performance/eval_golden.ipynb
MICA/analysis/evaluation/clustering_performance/eval_scnapy.py
MICA/analysis/evaluation/clustering_performance/scatter_plot_true_label.py
MICA/analysis/evaluation/clustering_performance/utils.py
MICA/analysis/evaluation/clustering_performance/Activity/PBMC_20k_CD4T.R
MICA/analysis/evaluation/clustering_performance/Activity/PBMC_20k_global.R
MICA/analysis/evaluation/clustering_performance/Activity/eval_PBMC_20k.py
MICA/analysis/evaluation/clustering_performance/Activity/marker_score_MICA_PBMC_14k.R
MICA/analysis/evaluation/clustering_performance/Activity/network_QC.R
MICA/analysis/evaluation/clustering_performance/GoldenStd/__init__.py
MICA/analysis/evaluation/clustering_performance/GoldenStd/debug_Buettner.py
MICA/analysis/evaluation/clustering_performance/GoldenStd/eval_Buettner.py
MICA/analysis/evaluation/clustering_performance/GoldenStd/eval_Goolam.py
MICA/analysis/evaluation/clustering_performance/GoldenStd/eval_Kolod.py
MICA/analysis/evaluation/clustering_performance/GoldenStd/eval_PBMC_20K.py
MICA/analysis/evaluation/clustering_performance/GoldenStd/eval_Pollen.py
MICA/analysis/evaluation/clustering_performance/GoldenStd/eval_Yan.py
MICA/analysis/evaluation/clustering_performance/LCA/LCA.vs.MICA.R
MICA/analysis/evaluation/clustering_performance/SC3/Rplots.pdf
MICA/analysis/evaluation/clustering_performance/SC3/cmd.sh
MICA/analysis/evaluation/clustering_performance/SC3/eval_Buettner.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Chung.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Goolam.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Klein.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Kolod.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_PBMC_14k.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_PBMC_20k.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Pollen.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Tasic.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Usoskin.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Yan.R
MICA/analysis/evaluation/clustering_performance/SC3/eval_Zeisel.R
MICA/analysis/evaluation/clustering_performance/SC3/psub.sh
MICA/analysis/evaluation/clustering_performance/SC3/psub2.sh
MICA/analysis/evaluation/clustering_performance/SC3/tracker_cmd.2021.07.13.err
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MICA/analysis/evaluation/clustering_performance/SC3/logs/out.129543324.1.txt
MICA/analysis/evaluation/clustering_performance/SC3/logs/out.129876155.1.txt
MICA/analysis/evaluation/clustering_performance/SC3/logs/out.129949313.1.txt
MICA/analysis/evaluation/clustering_performance/SC3/logs/out.129955182.1.txt
MICA/analysis/evaluation/clustering_performance/SC3/logs/out.129957014.1.txt
MICA/analysis/evaluation/clustering_performance/SC3/logs/out.129962976.1.txt
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MICA/analysis/evaluation/clustering_performance/SC3/logs/out.145305642.1.txt
MICA/analysis/evaluation/clustering_performance/SC3/logs/out.145930138.1.txt
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Buettner.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Chung.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Goolam.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Human_Motor_Cortex.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Klein.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Kolod.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_PBMC_14k.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_PBMC_20k.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Pollen.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Tasic.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Usoskin.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Yan.py
MICA/analysis/evaluation/clustering_performance/Scanpy/eval_Zeisel.py
MICA/analysis/evaluation/clustering_performance/Seurat/Rplots.pdf
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Buettner.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Chung.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Goolam.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Human_Motor_Cortex.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Human_Motor_Cortex.bash
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MICA/analysis/evaluation/clustering_performance/Seurat/eval_Klein.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Kolod.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_PBMC_20K.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Pollen.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Tasic.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Usoskin.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Yan.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_Zeisel.R
MICA/analysis/evaluation/clustering_performance/Seurat/eval_seurat.R
MICA/analysis/evaluation/clustering_performance/SilverStd/__init__.py
MICA/analysis/evaluation/clustering_performance/SilverStd/debug_Klein.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_1.3_million.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_Chung.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_Human_cortex.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_Klein.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_PBMC_12k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_PBMC_14k.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_PBMC_20K.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_PBMC_20k_filter_Ts.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_Tasic.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_Usoskin.py
MICA/analysis/evaluation/clustering_performance/SilverStd/eval_Zeisel.py
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_MICA_PBMC_12k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_MICA_PBMC_14k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_MICA_PBMC_16k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_MICA_PBMC_20k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_Scanpy_PBMC_20k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_seurat_PBMC_12k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_seurat_PBMC_14k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_seurat_PBMC_16k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/marker_score_seurat_PBMC_20k.R
MICA/analysis/evaluation/clustering_performance/SilverStd/singleR_seurat_PBMC_12k.R
MICA/analysis/evaluation/computing_performance/MI_fast.ipynb
MICA/analysis/evaluation/computing_performance/Numba.ipynb
MICA/analysis/evaluation/computing_performance/PBMC_12k.py
MICA/analysis/evaluation/computing_performance/PBMC_33k_mem_profile.py
MICA/analysis/evaluation/computing_performance/__init__.py
MICA/analysis/evaluation/computing_performance/benchmark_EU-kNN.py
MICA/analysis/evaluation/computing_performance/benchmark_MI-kNN.py
MICA/analysis/evaluation/computing_performance/benchmark_pecanpy.py
MICA/analysis/evaluation/computing_performance/benchmark_plot.py
MICA/analysis/evaluation/computing_performance/benchmark_summary.py
MICA/analysis/evaluation/computing_performance/bsub_benchmark_EU-kNN.sh
MICA/analysis/evaluation/computing_performance/bsub_benchmark_MI-kNN.sh
MICA/analysis/evaluation/computing_performance/bsub_benchmark_pecanpy.sh
MICA/analysis/evaluation/computing_performance/million.ipynb
MICA/analysis/evaluation/mutual_information/MI_raw.py
MICA/analysis/evaluation/optimal_k/silhouette.py
MICA/analysis/evaluation/preprocessing/10X_1.3_Million_Brain_Cells_from_E18_Mice.py
MICA/analysis/evaluation/preprocessing/GSE75688_Chung.py
MICA/analysis/evaluation/preprocessing/GoldernStd.py
MICA/analysis/evaluation/preprocessing/Goolam.oy.py
MICA/analysis/evaluation/preprocessing/Klein.py
MICA/analysis/evaluation/preprocessing/PBMC_33k.py
MICA/analysis/evaluation/preprocessing/PBMC_3k.py
MICA/analysis/evaluation/preprocessing/Pollen.R
MICA/analysis/evaluation/preprocessing/Pollen.py
MICA/analysis/evaluation/preprocessing/format_true_label.py
MICA/analysis/evaluation/preprocessing/human_cotex.py
MICA/analysis/evaluation/preprocessing/motor_cortex_human.R
MICA/analysis/evaluation/preprocessing/preprocess_ecoCART.py
MICA/analysis/evaluation/resolution/resolution_transformation.py
MICA/analysis/evaluation/silhouette/Buettner.py
MICA/analysis/evaluation/silhouette/Chung.py
MICA/analysis/evaluation/silhouette/Goolam.py
MICA/analysis/evaluation/silhouette/Klein.py
MICA/analysis/evaluation/silhouette/Kolod.py
MICA/analysis/evaluation/silhouette/PBMC_20k.py
MICA/analysis/evaluation/silhouette/Pollen.py
MICA/analysis/evaluation/silhouette/Usoskin.py
MICA/analysis/evaluation/silhouette/Yan.py
MICA/analysis/evaluation/silhouette/Zeisel.py
MICA/analysis/plots/ARI_barplot_pvalue.py
MICA/analysis/plots/ARI_summary.py
MICA/analysis/plots/__init__.py
MICA/analysis/plots/dataset_selected.py
MICA/analysis/plots/scatter_plot_true_label.py
MICA/analysis/plots/silhouette_barplot_pvalue.py
MICA/bin/__init__.py
MICA/bin/calc_scatter.py
MICA/bin/clustering.py
MICA/bin/graph_clustering.py
MICA/bin/merge_and_norm.py
MICA/bin/prep.py
MICA/bin/transform.py
MICA/config/config_cwlexec.json
MICA/cwl/calc_MI_pair.cwl
MICA/cwl/clustering.cwl
MICA/cwl/dim_reduce.cwl
MICA/cwl/graph_clustering.cwl
MICA/cwl/merge_and_norm.cwl
MICA/cwl/mica.cwl
MICA/cwl/mica_g.cwl
MICA/cwl/prep.cwl
MICA/lib/__init__.py
MICA/lib/activity.py
MICA/lib/aux_utils.py
MICA/lib/clustering.py
MICA/lib/consensus.py
MICA/lib/dimension_reduction.py
MICA/lib/distance.py
MICA/lib/neighbor_graph.py
MICA/lib/preprocessing.py
MICA/lib/silhouette.py
MICA/lib/utils.py
MICA/lib/visualize.py
conda/build.sh
conda/conda_build_config.yaml
conda/meta.yaml
images/MICA_workflow.png
test_data/inputs/Buettner_MICA_input.txt
test_data/inputs/PBMC_Demo_MICA_input_mini.txt
test_data/inputs/Yan_MICA_input.txt
test_data/inputs/10x/PBMC/3k/filtered_gene_bc_matrices/hg19/barcodes.tsv
test_data/inputs/10x/PBMC/3k/filtered_gene_bc_matrices/hg19/genes.tsv
test_data/inputs/10x/PBMC/3k/filtered_gene_bc_matrices/hg19/matrix.mtx
test_data/inputs/10x/PBMC/3k/pre-processed/pbmc3k_preprocessed.h5ad
test_data/outputs/mica.yml
test_data/outputs/Buettner/._clustering_UMAP_euclidean_20_3.png
test_data/outputs/Buettner/._clustering_UMAP_euclidean_20_3.txt
test_data/outputs/Buettner/._silhouette_20_3.pdf
test_data/outputs/Buettner/._silhouette_20_4.pdf
test_data/outputs/cwl_lsf/mica.yml
tests/test_MICA_Buettner.sh
tests/test_MICA_Yan.sh
tests/test_MICA_ge.sh
tests/test_MICA_local.sh
tests/test_MICA_local_graph.sh
tests/test_MICA_local_h5ad.sh
tests/test_MICA_lsf_h5ad_pbmc33k.sh
tests/test_MICA_lsf_h5ad_pbmc3k.sh
tests/test_MICA_lsf_rerun.sh
tests/test_MICA_pca.sh
tests/test_MICA_umap.sh
tests/test_all_units.sh
tests/test_calc_ARI.py
tests/test_calc_scatter.py
tests/test_clustering.py
tests/test_merge_and_norm.py
tests/test_mica_acceptance.py
tests/test_prep.py
tests/test_transform.py
tests/answerkey/cwl_local_k4_tsne_ClusterMem.txt
tests/answerkey/calc_scatter/test_mi_04.h5
tests/answerkey/clustering/Buettner_true_label.txt
tests/answerkey/clustering/Kolod_true_label.txt
tests/answerkey/clustering/Yan_true_label.txt
tests/answerkey/merge_and_norm/test_dist.h5
tests/answerkey/merge_and_norm/test_mi_whole.h5
tests/answerkey/prep/test.sliced.h5
tests/answerkey/prep/test.whole.h5
tests/answerkey/prep/test_mi_0.h5.tmp
tests/answerkey/prep/test_mi_1.h5.tmp
tests/answerkey/prep/test_mi_2.h5.tmp
tests/answerkey/transform/test_reduced.h5
tests/inputs/PBMC_Demo_MICA_input_mini.txt
tests/inputs/test_dist.h5
tests/inputs/test_mi_04.h5.tmp
tests/inputs/test_reduced.h5
tests/inputs/merge_and_norm/test_mi_0.h5
tests/inputs/merge_and_norm/test_mi_1.h5
tests/inputs/merge_and_norm/test_mi_2.h5