.gitignore
LICENSE
README.md
setup.py
Catactor/__init__.py
Catactor/mini_catactor.py
Catactor/pseudo_bulk.py
Catactor.egg-info/PKG-INFO
Catactor.egg-info/SOURCES.txt
Catactor.egg-info/dependency_links.txt
Catactor.egg-info/top_level.txt
LassoVariants/.gitignore
LassoVariants/LICENSE
LassoVariants/README.md
LassoVariants/AlternateLasso/AlternateLinearModel.py
LassoVariants/AlternateLasso/LICENSE
LassoVariants/AlternateLasso/README.md
LassoVariants/AlternateLasso/example/example_classification.py
LassoVariants/AlternateLasso/example/example_regression.py
LassoVariants/AlternateLasso/paper/paper_news20_task1.py
LassoVariants/AlternateLasso/paper/paper_news20_task2.py
LassoVariants/EnumLasso/EnumerateLinearModel.py
LassoVariants/EnumLasso/LICENSE
LassoVariants/EnumLasso/README.md
LassoVariants/EnumLasso/example/example_classification.py
LassoVariants/EnumLasso/example/example_regression.py
LassoVariants/EnumLasso/paper/paper_news20.py
LassoVariants/EnumLasso/paper/paper_synthetic_alpha.py
LassoVariants/EnumLasso/paper/paper_synthetic_rho.py
LassoVariants/EnumLasso/paper/paper_thaliana.py
LassoVariants/EnumLasso/paper/data/call_method_32.b
LassoVariants/EnumLasso/paper/data/call_method_32_ecotype_meta_info.tsv
LassoVariants/EnumLasso/paper/data/phenotype_published_raw.tsv
data/Mus_musculus_sorted_trans.GRCm38.96.gtf
data/Mus_musculus_sorted_trans_tss_1m.GRCm38.96.gtf
data/marker_name_list.csv
data/mm.en.et.csv
data/mm10.blacklist.bed
data/mouse_permissive_enhancers_phase_1_and_2_mm10.bed
data/cluster_annotation/BICCN2_cluster_annotation.txt
data/cluster_annotation/BICCN2_cluster_celltype_annotation.csv
data/cluster_annotation/BICCN2_rna_cluster_celltype_annotation.csv
data/cluster_annotation/GSE111586_cluster_celltype_annotation.csv
data/cluster_annotation/GSE111586_icluster_celltype_annotation.csv
data/cluster_annotation/GSE123576_cluster_celltype_annotation.csv
data/cluster_annotation/GSE126074_cluster_celltype_annotation.csv
data/cluster_annotation/GSE126074_cluster_celltype_annotation_auto.csv
data/cluster_annotation/GSE126074_icluster_celltype_annotation.csv
data/cluster_annotation/GSE127257_cluster_celltype_annotation.csv
data/cluster_annotation/GSE1303990_cluster_celltype_annotation.csv
data/cluster_annotation/README.md
data/metadata/GSE111586/.gitkeep
example/mini_catactor_tutorial.ipynb
example/preprocessing.ipynb
example/tutorial.ipynb
marker_genes/CU_markers/cusanovich2018_ext.txt
marker_genes/CU_markers/cusanovich2018_gli.txt
marker_genes/CU_markers/cusanovich2018_inh.txt
marker_genes/SC_markers/top_GABAergic_markers_fc_top.txt
marker_genes/SC_markers/top_Glutamatergic_markers_fc.txt
marker_genes/SC_markers/top_Non.Neuronal_markers_fc.txt
marker_genes/SF_markers/GABAergic_markers_fc.txt
marker_genes/SF_markers/Glutamatergic_markers_fc.txt
marker_genes/SF_markers/Non.Neuronal_markers_fc.txt
marker_genes/SF_subtype_markers/excitatory_L2.3.IT.txt
marker_genes/SF_subtype_markers/excitatory_L2.3.IT_location.bed
marker_genes/SF_subtype_markers/excitatory_L5.6.NP.txt
marker_genes/SF_subtype_markers/excitatory_L5.6.NP_location.bed
marker_genes/SF_subtype_markers/excitatory_L5.ET.txt
marker_genes/SF_subtype_markers/excitatory_L5.ET_location.bed
marker_genes/SF_subtype_markers/excitatory_L5.IT.txt
marker_genes/SF_subtype_markers/excitatory_L5.IT_location.bed
marker_genes/SF_subtype_markers/excitatory_L6.CT.txt
marker_genes/SF_subtype_markers/excitatory_L6.CT_location.bed
marker_genes/SF_subtype_markers/excitatory_L6.IT.Car3.txt
marker_genes/SF_subtype_markers/excitatory_L6.IT.Car3_location.bed
marker_genes/SF_subtype_markers/excitatory_L6b.txt
marker_genes/SF_subtype_markers/excitatory_L6b_location.bed
marker_genes/SF_subtype_markers/excitatory_markers_fc.txt
marker_genes/SF_subtype_markers/gabaergic_Lamp5.txt
marker_genes/SF_subtype_markers/gabaergic_Lamp5_location.bed
marker_genes/SF_subtype_markers/gabaergic_Pvalb.txt
marker_genes/SF_subtype_markers/gabaergic_Pvalb_location.bed
marker_genes/SF_subtype_markers/gabaergic_Sncg.txt
marker_genes/SF_subtype_markers/gabaergic_Sncg_location.bed
marker_genes/SF_subtype_markers/gabaergic_Sst.txt
marker_genes/SF_subtype_markers/gabaergic_Sst_location.bed
marker_genes/SF_subtype_markers/gabaergic_Vip.txt
marker_genes/SF_subtype_markers/gabaergic_Vip_location.bed
marker_genes/SF_subtype_markers/gabaergic_markers_fc.txt
marker_genes/SF_subtype_markers/cluster_annotation/BICCN2_cluster_annotation.txt
marker_genes/SF_subtype_markers/cluster_annotation/BICCN2_cluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/BICCN2_rna_cluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE111586_cluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE111586_icluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE123576_cluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE126074_cluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE126074_cluster_celltype_annotation_auto.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE126074_icluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE127257_cluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/GSE1303990_cluster_celltype_annotation.csv
marker_genes/SF_subtype_markers/cluster_annotation/old_GSE111586_cluster_celltype_annotation.csv
marker_genes/TA_markers/tasic2016.txt
marker_genes/TA_markers/tasic2016_gaba.txt
marker_genes/TA_markers/tasic2016_gaba_mat.txt
marker_genes/TA_markers/tasic2016_gli.txt
marker_genes/TA_markers/tasic2016_gli_mat.txt
marker_genes/TA_markers/tasic2016_glu.txt
marker_genes/TA_markers/tasic2016_glu_mat.txt
marker_genes/TA_markers/tasic2016_mat.txt
marker_genes/TN_markers/.DS_Store
marker_genes/TN_markers/README.md
marker_genes/TN_markers/tasic2018_gaba.txt
marker_genes/TN_markers/tasic2018_gli.txt
marker_genes/TN_markers/tasic2018_glu.txt
marker_genes/others/biccn_atac.txt
marker_genes/others/chen2019.txt
marker_genes/others/hvg.txt
marker_genes/others/marker_name_list.csv
marker_genes/others/rank_gene_list_celltype.csv
marker_genes/others/spektor2019.txt
output/average_profile/.gitkeep
output/scobj/.gitkeep
script/data_annotation/annotate_cluster.py
script/data_annotation/annotation.sh
script/data_annotation/annotation_metadata.R
script/data_annotation/produce_BICCN2_rna_ann.py
script/data_processing/biccn_data_reading.py
script/data_processing/data_preprocess.R
script/data_processing/data_preprocess.py
script/data_processing/merge_cistopic_cluster.py
script/data_processing/snap_atac_to_text.R
script/joint_clustering/bbknn_training.py
script/joint_clustering/parse_auroc_from_seurat.py
script/joint_clustering/read_pickle_data.py
script/joint_clustering/seurat_jc.R
script/misc/check_scobj.py
script/misc/convert_ave_to_bed.py
script/misc/extract_marker_region.py
script/visualization/compare_down_sampled_auc.py
script/visualization/marker_gene_plot.py
script/visualization/plot_auc_detailed_celltype.py
script/visualization/plot_auc_each_signal.py
script/visualization/plot_auroc_rank.R
script/visualization/plot_heatmap.R
script/visualization/plot_raw_gene_auc.py
script/visualization/plot_training_result.py
script/visualization/upset_plot.R
script/visualization/visualize_consistency_cells.py
shell_scripts/visualization_GSE111586_cortex.sh
shell_scripts/prediction/predict_BICCN.sh
shell_scripts/prediction/predict_GSE111586_distal.sh
shell_scripts/prediction/predict_GSE123576_distal.sh
shell_scripts/prediction/predict_GSE126074_distal.sh
shell_scripts/prediction/predict_GSE126074_rna.sh
shell_scripts/prediction/predict_GSE127257_distal.sh
shell_scripts/prediction/predict_GSE1303990_distal.sh
shell_scripts/prediction/predict_GSE1303990_rna.sh
shell_scripts/preprocessing/visualization_BICCN_distal.sh
shell_scripts/preprocessing/visualization_GSE100033_distal.sh
shell_scripts/preprocessing/visualization_GSE111586_distal.sh
shell_scripts/preprocessing/visualization_GSE123576_distal.sh
shell_scripts/preprocessing/visualization_GSE126074_distal.sh
shell_scripts/preprocessing/visualization_GSE127257_distal.sh
shell_scripts/preprocessing/visualization_GSE1303990_distal.sh
shell_scripts/preprocessing_one_to_multi/visualization_BICCN_multi.sh
shell_scripts/preprocessing_one_to_multi/visualization_GSE111586_multi.sh
shell_scripts/preprocessing_one_to_multi/visualization_GSE123576_multi.sh
shell_scripts/preprocessing_one_to_multi/visualization_GSE126074_multi.sh
shell_scripts/preprocessing_one_to_multi/visualization_GSE1303990_multi.sh
shell_scripts/preprocessing_rna/visualization_BICCN_rna.sh
shell_scripts/preprocessing_rna/visualization_GSE126074_rna.sh
shell_scripts/preprocessing_rna/visualization_GSE1303990_rna.sh
src/Catactor
src/Catactor_base.py
src/Catactor_utils.py
src/learn_alternate.py
test/.gitkeep
test/test.py