Frequently Asked Questions (FAQ)

This section provides answers to some common questions regarding the NiCo library.

  1. What is NiCo?

  1. NiCo is a Python library designed for spatial transcriptomics analysis. It provides modules for cell type annotation, niche interaction inference, and covariation analysis within the niche cell types in spatial transcriptomics data.

  1. How do I install NiCo?

  1. You can install NiCo using pip or just keep the python scripts available at github in your analysis path. For detailed installation instructions, refer to the Installation section.

  1. What types of data does NiCo support?

  1. NiCo supports imaging- or sequencing-based spatial transcriptomics data. It requires an expression matrix in scTransform-like normalization, typically stored in an AnnData object.

  1. How can I annotate cell types in my spatial data?

  1. You can use the Annotations module provided by NiCo. The find_anchor_cells_between_ref_and_query and nico_based_annotation functions help perform cell type annotation. Refer to the Examples section for a detailed example.

  1. How do I visualize cell type annotations?

  1. NiCo offers several visualization functions in the Annotations module, such as visualize_umap_and_cell_coordinates_with_all_celltypes and visualize_umap_and_cell_coordinates_with_selected_celltypes. These functions help visualize expression UMAP and cell coordinates for the annotated cell types.

  1. Can NiCo infer niche interactions?

  1. Yes, the Interactions module of NiCo provides functions for inferring significant niche cell type interactions, such as spatial_neighborhood_analysis and plot_niche_interactions_with_edge_weight.

  1. What is the purpose of covariation analysis?

  1. Covariation analysis identifies significance cell state covariations between a central cell type and its niche cell types using latent factors. The Covariations module in NiCo offers tools like gene_covariation_analysis and plot_cosine_and_spearman_correlation_to_factors for this purpose.

  1. How can I perform ligand-receptor interaction analysis?

  1. The Covariations module provides functions like save_LR_interactions_in_excelsheet_and_regression_summary_in_textfile_for_interacting_cell_types and find_LR_interactions_in_interacting_cell_types for analyzing ligand-receptor interactions between covarying cell types.

  1. Where can I find detailed usage examples and tutorials?

  1. Refer to the Examples section for detailed usage examples covering the main functionalities of NiCo and github links for the tutorials.

  1. Who can I contact for support?

  1. For support, you can open an issue on the project’s GitHub repository or contact the maintainers directly through the provided contact information on the repository page.

  1. Is there a way to contribute to NiCo?

  1. Yes, contributions are welcome! You can contribute by reporting issues, suggesting new features, or submitting pull requests on the project’s GitHub repository.