Welcome to SPOT’s documentation!

SPOT (Spatial Perturbation Omics analysis Toolkit) is a model based toolkit for spaital CRISPR knockout screening analysis.

SPOT is a free, open-source software for both python and R environment users under the MIT license. Please cite the paper Paper here when using the toolkit.

Offcial documentation can be found here at <https://spot-tutorial.readthedocs.io/en/latest/>

Refer to our SPAC-seq analysis tutorial <https://github.com/pkuTrasond/SPAC-seq/tree/master>, it offers a simple and intuitive API.

Check out the Usage section for further information, including how to Installing using python the project.

Note

This project is under active development.

Contents

• Preprocessing
  • Preprocessing
    • filter_guide_reads()
• NMF
  • A_preprocessing.nmf_clustering()
  • A_preprocessing.nmf_consensus()
• Cellcharter
  • cluster_cellcharter()
• ClusterDependent
  • CLuster PERMANOVA
    • rank_by_cluster_permanova()
  • Chi-square Test Ranking
    • rank_by_chi_square()
• ClusterIndependent
  • Kernel Density Estimation and Wasserstein Distance
    • rank_by_kernel_estimated_distance()
  • KL Distance Ranking
    • rank_by_relative_entropy()
• Tutorial
  • Preparations
  • Importing necessary libraries
  • Preprocessing
  • Clustering
  • Cluster Dependent Analysis
  • Cluster Independent Analysis