CellOracle

Tutorial — celloracle 0.10.13 documentation (morris-lab.github.io)https://morris-lab.github.io/CellOracle.documentation/tutorials/index.html

1. Main CellOracle analysis

• GRN model construction and network analysis: This notebook introduces how to construct sample-specific GRN models. It also contains examples of network analyses that use graph theory.

• In silico gene perturbation with GRNs : This notebook performs in silico gene perturbation analysis using GRN models.

 

2. How to prepare input data

We recommend getting started with CellOracle using the provided demo dataset. When you want to apply CellOracle to your own scRNA-seq or scATAC-seq dataset, please refer to the following tutorials to learn how to prepare input data.

• scRNA-seq data preparation: This notebook explains the preprocessing steps for scRNA-seq data.

• Base GRN input data preparation: This tutorial explains how to prepare the input data for TF motif scanning.

• Transcription factor binding motif scan: This tutorial describes the TF motif scan pipeline for base-GRN construction.

Index

GRN model construction and network analysis

• 1. GRN model construction and network analysis
  • Overview
  • 0. Import libraries
  • 1. Load data
  • 2. Make Oracle object
  • 3. KNN imputation
  • 4. Save and Load.
  • 5. GRN calculation
  • 6. Network preprocessing
  • 7. Network analysis; Network score for each gene
  • 8. Network analysis; network score distribution

In silico gene perturbation with GRNs

• 1. In silico gene perturbation with GRNs
  • Overview
  • 0. Import libraries
  • 1. Load data
  • 2. Make predictive models for simulation
  • 3. In silico TF perturbation analysis
  • 4. Visualization
  • 5. [This step is optional] Compare simulation vector with development vectors
  • 6. Focus on a single development lineage to interpret the results in detail

Prepare input data

• 1. scRNA-seq data preparation
  • Overview
  • A. scRNA-seq data preprocessing with Scanpy
  • B. scRNA-seq data preprocessing with Seurat
• 2. Pseudotime calculation
  • Overview
  • 0. Import libraries
  • 1. Load data
  • 2. Pseudotime calculation
  • 3. Save data
• 3. Base GRN input data preparation
  • Overview
  • Option1. Preprocessing scATAC-seq data
  • Option2. Data preprocessing of bulk ATAC-seq data

TF motif scan for base-GRN construction

• 1. Transcription factor binding motif scan
  • Scan DNA sequences searching for TF binding motifs
• 2. How to use custom motif data
  • gimmemotifs motif data
  • CellOracle motif dataset generated from the CisBP version2 database
  • How to create custom motif data

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