├── LICENSE ├── README.md ├── bin ├── LIGER_integration.R ├── alignment_score.py ├── concat_by_homology_multiple_species_by_gene_id.R ├── concat_by_homology_rligerUINMF_multiple_species.R ├── convert_format.R ├── fastMNN_integration.R ├── harmony_integration.py ├── kbet_multiple_species.R ├── rliger_integration_UINMF_multiple_species.R ├── scANVI_integration.py ├── scIB_metrics.py ├── scIB_metrics_individual.py ├── scIB_trajectory.py ├── scanorama_integration.py ├── sccaf_assessment_metadata.py ├── sccaf_kNN_distance.py ├── sccaf_projection_multiple_species.py ├── scvi_integration.py ├── seurat_CCA_integration.R ├── seurat_RPCA_integration.R └── validate_input.py ├── concat_by_homology_multiple_species.nf ├── config └── example.config ├── containers └── README.md ├── cross_species_assessment_multiple_species_individual.nf ├── cross_species_integration_multiple_species.nf ├── dockerfiles ├── ALCS.Dockerfile ├── scanpy.Dockerfile └── seurat.Dockerfile ├── envs ├── sceasy.yml ├── scib.yml 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