Welcome to TARDIS’s documentation!

TARDIS (TArget pRioritization toolkit for CRISPR Data In Spatial-omics) is a model based toolkit for tissue-specific CRISPR knockout screening analysis.

Citation

For usage, please refer to the CELL paper Uncovering Spatially Resolved Functional Genomics with CRISPR Screen Sequencing.. Please cite the paper when using the toolkit.

TARDIS is a free, open-source software for both python and R environment users under the MIT license.

Official documentation can be found here.

Refer to our SPAC-seq website for data download and analysis at https://spac.pku-genomics.org.

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

Note

This project is under active development.

Contents

• Installation
  • Installing using python
  • Installing using R
    • Install with devtools
    • Quick start
    • Python ↔ R API
• Preprocessing
  • Visium HD
    • Read Spaceranger output
  • Stereoseq
    • Read SAW output
      • tardis_spac.utils.load_bin()
  • TARDIS preprocessing functions
    • tardis_spac.utils.qc_guide_bins()
    • tardis_spac.utils.remove_mito_ribo_hk_lnc_genes()
    • tardis_spac.utils.filter_guide_reads()
    • tardis_spac.utils.combine_guide_replicates()
• NMF
  • Gene program NMF Principle
    • tardis_spac.utils.nmf_clustering()
    • tardis_spac.utils.nmf_consensus()
• Cellcharter
  • CellCharter-based Spatial Clustering
    • tardis_spac.external.cluster_cellcharter()
• GlobalModule
  • Kernel Density Estimation and Wasserstein Distance
  • Overview
  • Biological Rationale
  • Mathematical Principles
  • Function Documentation
    • wasserstein_distance()
  • KL Divergence-Based Ranking
    • kl_divergence()
• LocalModule
  • Guide Ranking by Cluster-Dependent Distribution
  • PERMANOVA-Based Clustering Guide Ranking
    • permanova()
  • Aitchison Distance-Based Guide Ranking
    • aitchison_distance()
  • Result Storage & Usage
• Plotting Functions
  • TARDIS Plotting API
  • Plot KDE of Ranking Results
    • tardis_spac.utils.plot_top_kde()
  • Spatial Plotting of Guides
    • tardis_spac.utils.plot_spatial_guides()
  • Tips and Interpretation
  • See Also
• Tutorial
  • Preparations
  • Infiltrated T cell library
    • Loading and preprocessing
    • Filtering and Quality Control
    • Kullback-Leibler divergence test
  • Perturbed subcutaneous tumor model
    • General quanlity control
    • Clone calling for tumor Models
    • Niche specific analysis

Contacts

If you have any questions or suggestions, please feel free to contact me at Barry Wang.