Tutorials¶

This page is the markdown overview for the tutorial structure defined in mkdocs.yml. It is meant to help readers scan the current OmicVerse tutorial map before jumping into notebooks or topic-specific guides.

Bulk¶

• Bulk tutorial index
• Upstream
• Bulk RNA-seq alignment with STAR
• Bulk RNA-seq alignment with kb-python
• Preprocessing
• Batch correction in Bulk RNA-seq or microarray data
• Downstream
• Different expression analysis
• Different expression analysis with DEseq2
• Protein-Protein interaction (PPI) analysis by String-db
• WGCNA (Weighted gene co-expression network analysis) analysis
• Deconvolution
• Bulk deconvolution with reference scRNA-seq
• Others
• TCGA database preprocess

Single¶

• Single-cell tutorial index
• Alignment
• Alignment of single-cell RNA-seq data
• Alignment of single-cell RNA-seq data for RNA velocity analysis
• Preprocessing
• Preprocessing the data of scRNA-seq [CPU]
• Preprocessing the data of scRNA-seq [GPU]
• Clustering space
• Data integration and batch correction
• Consensus Non-negative Matrix factorization (cNMF)
• Lazy analysis of scRNA-seq
• Annotation
• Reference-free automated single-cell cell type annotation
• Reference automated single-cell cell type annotation
• Automatic cell type annotation with GPT/Other
• Mapping Cell Names to the Cell Ontology
• Celltype auto annotation with SCSA
• Celltype auto annotation with MetaTiME
• Celltype annotation migration(mapping) with TOSICA
• Celltype auto annotation with scMulan
• Consensus annotation with CellVote
• Trajectory
• Prediction of absolute developmental potential using CytoTrace2
• Basic Trajectory Inference
• Trajectory Inference with StaVIA
• Timing-associated genes analysis with TimeFateKernel
• Identify the driver regulators of cell fate decisions
• Cell Structure
• Inference of MetaCell from Single-Cell RNA-seq
• Differential expression and celltype analysis [All Cell]
• Differential expression analysis [Meta Cell]
• Gene Regulatory Network Analysis with SCENIC
• Pathway analysis with AUCell
• Cell interaction with CellPhoneDB
• Drug response predict with scDrug
• Batch Correction with SIMBA
• Velocity
• Velocity Basic Calculation
• Velocity Optimization
• Multi-omics
• Multi omics analysis by MOFA
• Multi omics analysis by MOFA and GLUE
• Celltype annotation transfer in multi-omics

Bulk2Single¶

• Bulk2Single tutorial index
• Bulk RNA-seq generate 'interrupted' cells to interpolate scRNA-seq
• Bulk RNA-seq to Single RNA-seq
• Single RNA-seq to Spatial RNA-seq

Space¶

• Space tutorial overview
• Preprocess
• Crop and Rotation of spatial transcriptomic data
• Visium 10x HD Cellpose
• Analyze Nanostring data
• Analyze Visium HD data
• Spatial clustering and denoising expressions
• Spatial integration and clustering
• Deconvolution
• Identifying Pseudo-Spatial Map
• Spatial deconvolution with reference scRNA-seq
• FlashDeconv (fast, GPU-free deconvolution)
• Spatial deconvolution without reference scRNA-seq
• Downstream
• Spatial transition tensor of single cells
• Spatial Communication
• Spatial IsoDepth Calculation
• Single cell spatial alignment tools

Foundation Model¶

• Foundation model overview
• ov.fm API Overview
• ov.fm Quick Start
• Skill-ready models
• scGPT guide and tutorial
• Geneformer guide and tutorial
• UCE guide and tutorial
• scFoundation guide and tutorial
• CellPLM guide and tutorial
• Core and specialized models
• scBERT
• GeneCompass
• Nicheformer
• scMulan
• tGPT
• CellFM
• scCello
• scPRINT
• AIDO.Cell
• PULSAR
• Tabula
• ATACformer
• scPlantLLM
• LangCell
• Cell2Sentence
• GenePT
• ChatCell

Plotting¶

• Plotting tutorial overview
• Visualization of single cell RNA-seq
• Visualization of bulk RNA-seq
• Palette optimization for publication-quality single-cell & spatial plots
• Color system

OmicClaw¶

• General notebook / pipeline workflows
• J.A.R.V.I.S. with PBMC3k
• J.A.R.V.I.S. with Ten-Task Suite
• Gateway and channels
• Overview
• Setup and Auth
• Telegram Tutorial
• Feishu Tutorial
• iMessage Tutorial
• QQ Tutorial
• Session Workflow
• Common Issues
• Coding
• Overview and CLI
• OpenClaw Integration
• MCP server
• Overview
• Quick Start
• Full Start
• Tool Catalog
• Clients and Deployment
• Runtime and Troubleshooting
• Reference
• Claude Code Walkthrough