Tutorials

DIRAC primarily includes functionalities for both horizontal and vertical integration. This tutorial consists of the following sections:

1. Vertical Integration of DBiT-seq Data - In this section, we will introduce how to perform vertical integration of DBiT-seq data using DIRAC.

2. Horizontal Integration of DLPFC Data - This section will demonstrate how to conduct horizontal integration of DLPFC data to obtain a more comprehensive perspective.

3. Constructing the spatial domain structure of the mouse spleen (bin100) with DIRAC. - In this section, we will discuss how DIRAC integrates multi-omics data to unveil the spatial and functional dynamics of immune cells in the mouse spleen.

4. Constructing a Spatial Multi-Omics Atlas of Mouse Thymus (cellbin) with DIRAC - We will explore how to utilize DIRAC to construct a spatial multi-omics atlas of developing T cells in the mouse thymus to better understand their functions.

• Tutorial for spatial multi-omics vertical integration using DIRAC
  • Installation
  • Download the data
  • Load DBiT-seq data
  • Prepare to Integrate
  • Training DIRAC
  • Save data
• Horizontal integration on DLPFC using DIRAC
  • Download the data
  • Run DIRAC on Dorsolateral Prefrontal Cortex (Spatial transcriptomics)
  • Presentation of DIRAC results and comparison with other methods
    • Spatial domain presentation of DIRAC
    • Compare the ACC pirate plots of all methods
    • Draw ROC curve
    • Show UMAP on 151673 as test data
• Identify spatial domains in the mouse spleen (bin100) using DIRAC
  • Download the data （Under review, will be provided later）
  • DIRAC’s vertical integration of RNA + Protein data from the mouse spleen
  • Spatial domain names and differential gene and protein expression
  • Characterizing spatial domain profiles
  • Exploration of protein and RNA library size and feature autocorrelations
• Mouse spleen (cellbin) DIRAC for spatial localization of immune cells
  • Download the data （Under review, will be provided later）
  • Step 1: Align the cellbin data with the bin100 data using Stereopy
  • Step 2: Run the horizontal integration task of DIRAC
    • Step 2.1: ADT+RNA
    • Step 2.2: ADT only
    • Step 2.3: Only RNA
  • Step 3: Comparison of cell proportions, including CITE-seq, Stereo-CITE-seq (Joint, Only RNA, Only Protein)