omicverse Readthedocs
Api pl
GitHub
omicverse Readthedocs
GitHub
Index
Installation
Tutorial
Tutorial
Bulk
Bulk
Preprocessing
Preprocessing
Batch correction in Bulk RNA-seq or microarray data
Downstream
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
Deconvolution
Bulk deconvolution with reference scRNA-seq
Others
Others
TCGA database preprocess
Single
Single
Alignment
Alignment
Alignment and analysis of single-cell RNA-seq data
Alignment and RNA velocity analysis of single-cell RNA-seq data.
Preprocessing
Preprocessing
Preprocessing the data of scRNA-seq with omicverse[CPU-GPU-mixed]
Preprocessing the data of scRNA-seq with omicverse[GPU]
Clustering space
Data integration and batch correction
Consensus Non-negative Matrix factorization (cNMF)
Lazy analysis of scRNA-seq
Annotation
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/Taxonomy
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
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
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-cell communication using CellPhoneDBViz
Drug response predict with scDrug
Data integration and batch correction with SIMBA
Velocity
Velocity
Velocity Basic Calculation
Velocity Optimization
Multi omics
Multi omics
Multi omics analysis by MOFA
Multi omics analysis by MOFA and GLUE
Celltype annotation transfer in multi-omics
Bulk2Single
Bulk2Single
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
Preprocess
Preprocess
Crop and Rotation of spatial transcriptomic data
Cell Segmemtation (10x HD)
Spatial clustering and denoising expressions
Spatial integration and clustering
Deconvolution
Deconvolution
Identifying Pseudo-Spatial Map
Spatial deconvolution with reference scRNA-seq
Spatial deconvolution without reference scRNA-seq
Downstream
Downstream
Spatial transition tensor of single cells
Spatial Communication
Spatial IsoDepth Calculation
Single cell spatial alignment tools
LLM
LLM
Domain Research (dr): Comprehensive Report Tutorial
Domain Research (dr) — Live Web
ov.Agent with Skills: Natural‑Language Single‑Cell Analysis (PBMC3k)
UCE
scGPT
scFoundation
GeneFormer
CellPLM
Plotting
Plotting
Visualization of single cell RNA-seq
Visualization of Bulk RNA-seq
Color system
GPU Support
API documentation
Release notes
Developer guild
Api pl