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OmicVerse Documentation
OmicVerse Installation Guide
Tutorials
Bulk RNA-seq
Upstream
Bulk RNA-seq mapping with STAR
Bulk RNA-seq mapping 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
Metabolomics
Metabolomics preprocessing and univariate statistics
Multivariate discrimination with PLS-DA and OPLS-DA
Metabolite-set enrichment analysis (MSEA)
Untargeted LC-MS and mummichog pathway inference
Lipidomics with LIPID MAPS and LION
Batch effect and drift correction for LC-MS
Multi-factor designs — ASCA and linear mixed models
Biomarker discovery — univariate AUC + multivariate panel
Differential correlation — DGCA
Multi-omics integration — metabolomics + RNA-seq with MOFA
Real-data case study — MTBLS1 (urine NMR, Type 2 Diabetes)
Microbiome
16S rRNA amplicon analysis with OmicVerse
16S phylogeny: MAFFT → FastTree → Faith PD + UniFrac
DADA2 backend: pure-Python ASV inference
Differential abundance: Wilcoxon vs DESeq2 vs ANCOM-BC
Cross-cohort 16S meta-analysis
Single-Cell RNA-seq
Alignment
Alignment and analysis of single-cell RNA-seq data
Alignment and RNA velocity analysis of single-cell RNA-seq data.
Preprocessing
Preprocessing the data of scRNA-seq with omicverse[CPU-GPU-mixed]
Preprocessing the data of scRNA-seq with omicverse[GPU]
Preprocessing the data of scRNA-seq [Rust / out-of-memory]
Clustering space
Data integration and batch correction
GeneModule Identified
Lazy analysis of scRNA-seq
Annotation
Reference-free automated single-cell cell type annotation
Reference automated single-cell cell type annotation
Consensus annotation with CellVote — PBMC3k
Mapping Cell Names to the Cell Ontology/Taxonomy
Individual methods
MetaCell
MetaCell
Recommended workflow: SEACells end-to-end + downstream sanity
Multi-sample metacells with batch correction
MetaCell zoo
SEACells — kernel archetypal analysis
MetaQ — VQ-VAE codebook metacells
SuperCell — kNN graph + walktrap community detection
k-means — the trivial baseline that’s often hard to beat
random — the honest lower-bound baseline
GeoSketch — density-aware sketching as a metacell baseline
Side-by-side comparison of all metacell backends
Trajectory
Prediction of absolute developmental potential using CytoTrace2
Trajectory Inference with Diffusion Map and PAGA
Trajectory Inference with Slingshot
Trajectory Inference with Palantir
Trajectory Inference with scTour
Trajectory Inference with Monocle 2 on the Olsson Hematopoiesis Dataset
Trajectory Inference with StaVIA
Trajectory Inference with VIA and scVelo
Timing-associated genes analysis with TimeFateKernel
Identify the driver regulators of cell fate decisions
Cell-Cell Communication
Cell-cell communication analysis with CellPhoneDB
Cell-cell communication analysis with LIANA+
Cell Structure
Differential expression and celltype analysis [All Cell]
Differential expression analysis [Meta Cell]
Gene Regulatory Network Analysis with SCENIC
Drug response predict with scDrug
Data integration and batch correction with SIMBA
Copy-Number Variation
Single-cell copy-number variation with CopyKAT
Single-cell copy-number variation with inferCNV
Enrichment
Pathway analysis with AUCell
Comparing enrichment-score methods on scRNA-seq
Velocity
Velocity Basic Calculation
Velocity Optimization
Velocity-guided CellRank Analysis
Multi-omics
Multi omics analysis by MOFA
Multi omics analysis by MOFA and GLUE
Celltype annotation transfer in multi-omics
Multi-Omics
Bulk RNA-seq generate ‘interrupted’ cells to interpolate scRNA-seq
Bulk RNA-seq to Single RNA-seq
Single RNA-seq to Spatial RNA-seq
Paired microbe ↔ metabolite integration (Franzosa 2019 IBD)
Spatial Transcriptomics
Preprocessing
Crop and Rotation of spatial transcriptomic data
Cell Segmentation (10x HD)
Analyze NanoString data
Analyze Xenium data
Analyze 10x Atera (WTA Preview) FFPE breast cancer data
Analyze Visium HD data
Spatial integration and clustering
Clustering
Spatial clustering with GraphST + pymclustR
Spatial clustering with BINARY + pymclustR
Spatial clustering with STAGATE + pymclustR
Spatial clustering with CAST + pymclustR
Spatial clustering with BANKSY + pymclustR
Deconvolution
Identifying Pseudo-Spatial Map
Spatial deconvolution with reference scRNA-seq
Spatial deconvolution with RCTD
FlashDeconv: Fast Spatial Deconvolution via Structure-Preserving Sketching
Spatial deconvolution without reference scRNA-seq
Downstream
Spatial transition tensor of single cells
Spatial Communication
Spatial IsoDepth Calculation
Single cell spatial alignment tools
Foundation Models
Overview
Skill-Ready Models
scGPT
GeneFormer
UCE
scFoundation
CellPLM
Core Models
Specialized Models
Domain-Specific Models
Visualization & Plotting
Visualization of single cell RNA-seq
Visualization of Bulk RNA-seq
Palette optimization for publication-quality single-cell & spatial plots
Scientific plotting for publication with OmicVerse
Color system
Circular UMAP with plot1cell
OmicClaw
Gateway and Channels
OmicClaw Gateway Overview
OmicClaw Setup and Auth
OmicClaw Telegram Tutorial
OmicClaw Feishu 教程
OmicClaw iMessage Tutorial
OmicClaw QQ Tutorial
OmicClaw Session Workflow
OmicClaw Troubleshooting
MCP Server
OmicVerse MCP Server
OmicVerse MCP Quick Start
OmicVerse MCP Full Start
OmicVerse MCP Tool Catalog
OmicVerse MCP Clients and Deployment
OmicVerse MCP Runtime and Troubleshooting
OmicVerse MCP Reference
Using OmicVerse MCP with Claude Code — Step by Step
General Notebooks
J.A.R.V.I.S. with PBMC3k
J.A.R.V.I.S. with Ten-Task Suite
API Reference
User API
omicverse.generate_reference_table
omicverse.settings.cpu_gpu_mixed_init
omicverse.settings.gpu_init
omicverse.io.load
omicverse.io.read
omicverse.io.read_10x_h5
omicverse.io.read_10x_mtx
omicverse.io.read_csv
omicverse.io.read_h5ad
omicverse.io.read_nanostring
omicverse.io.read_visium_hd
omicverse.io.read_visium_hd_bin
omicverse.io.read_visium_hd_seg
omicverse.io.read_xenium
omicverse.io.save
omicverse.io.spatial.read_visium
omicverse.alignment.amplicon_16s_pipeline
omicverse.alignment.build_amplicon_anndata
omicverse.alignment.build_phylogeny
omicverse.alignment.bulk_rnaseq_pipeline
omicverse.alignment.count
omicverse.alignment.cutadapt
omicverse.alignment.dada2_pipeline
omicverse.alignment.fastp
omicverse.alignment.fasttree
omicverse.alignment.featureCount
omicverse.alignment.fetch_rdp
omicverse.alignment.fetch_silva
omicverse.alignment.fetch_sintax_ref
omicverse.alignment.fqdump
omicverse.alignment.mafft
omicverse.alignment.parallel_fastq_dump
omicverse.alignment.prefetch
omicverse.alignment.ref
omicverse.alignment.STAR
omicverse.pp.anndata_to_CPU
omicverse.pp.anndata_to_GPU
omicverse.pp.binary_search
omicverse.pp.champ
omicverse.pp.filter_cells
omicverse.pp.filter_genes
omicverse.pp.highly_variable_features
omicverse.pp.highly_variable_genes
omicverse.pp.identify_robust_genes
omicverse.pp.leiden
omicverse.pp.log1p
omicverse.pp.louvain
omicverse.pp.mde
omicverse.pp.neighbors
omicverse.pp.normalize_pearson_residuals
omicverse.pp.pca
omicverse.pp.preprocess
omicverse.pp.qc
omicverse.pp.recover_counts
omicverse.pp.regress
omicverse.pp.regress_and_scale
omicverse.pp.remove_cc_genes
omicverse.pp.scale
omicverse.pp.score_genes_cell_cycle
omicverse.pp.scrublet
omicverse.pp.scrublet_simulate_doublets
omicverse.pp.select_hvf_pegasus
omicverse.pp.sude
omicverse.pp.tsne
omicverse.pp.umap
omicverse.single.Annotation
omicverse.single.AnnotationRef
omicverse.single.auto_resolution
omicverse.single.autoResolution
omicverse.single.batch_correction
omicverse.single.CellOntologyMapper
omicverse.single.CellVote
omicverse.single.cNMF
omicverse.single.convert_human_to_mouse_network
omicverse.single.cosg
omicverse.single.cytotrace2
omicverse.single.DCT
omicverse.single.DEG
omicverse.single.download_cellphonedb_database
omicverse.single.download_cl
omicverse.single.Drug_Response
omicverse.single.dynamic_features
omicverse.single.factor_correlation
omicverse.single.factor_exact
omicverse.single.Fate
omicverse.single.find_markers
omicverse.single.format_liana_results
omicverse.single.gene_trends
omicverse.single.generate_scRNA_report
omicverse.single.geneset_aucell
omicverse.single.get_celltype_marker
omicverse.single.get_cluster_celltype
omicverse.single.get_markers
omicverse.single.get_obs_value
omicverse.single.get_weights
omicverse.single.GLUE_pair
omicverse.single.gptcelltype
omicverse.single.gptcelltype_local
omicverse.single.lazy
omicverse.single.load_human_prior_interaction_network
omicverse.single.MetaCell
omicverse.single.MetaTiME
omicverse.single.Monocle
omicverse.single.mouse_hsc_nestorowa16
omicverse.single.pathway_aucell
omicverse.single.pathway_aucell_enrichment
omicverse.single.pathway_enrichment
omicverse.single.pathway_enrichment_plot
omicverse.single.plot_metacells
omicverse.single.pyCEFCON
omicverse.single.pyMOFA
omicverse.single.pyMOFAART
omicverse.single.pySCSA
omicverse.single.pySIMBA
omicverse.single.pyTOSICA
omicverse.single.run_cellphonedb_v5
omicverse.single.run_liana
omicverse.single.scanpy_cellanno_from_dict
omicverse.single.SCENIC
omicverse.single.TrajInfer
omicverse.single.Velo
omicverse.bulk.batch_correction
omicverse.bulk.Deconvolution
omicverse.bulk.geneset_enrichment
omicverse.bulk.geneset_plot
omicverse.bulk.geneset_plot_multi
omicverse.bulk.Matrix_ID_mapping
omicverse.bulk.pyDEG
omicverse.bulk.pyGSEA
omicverse.bulk.pyPPI
omicverse.bulk.pyTCGA
omicverse.bulk.pyWGCNA
omicverse.bulk.readWGCNA
omicverse.bulk.string_interaction
omicverse.metabol.aggregate_by_class
omicverse.metabol.annotate_lipids
omicverse.metabol.annotate_peaks
omicverse.metabol.anova
omicverse.metabol.asca
omicverse.metabol.asca_variance_bar
omicverse.metabol.biomarker_panel
omicverse.metabol.blank_filter
omicverse.metabol.corr_network
omicverse.metabol.corr_network_plot
omicverse.metabol.cv_filter
omicverse.metabol.dgca
omicverse.metabol.dgca_class_bar
omicverse.metabol.differential
omicverse.metabol.drift_correct
omicverse.metabol.fetch_chebi_compounds
omicverse.metabol.fetch_hmdb_from_name
omicverse.metabol.fetch_kegg_pathways
omicverse.metabol.fetch_lion_associations
omicverse.metabol.impute
omicverse.metabol.lion_enrichment
omicverse.metabol.load_pathways
omicverse.metabol.map_ids
omicverse.metabol.meba
omicverse.metabol.mixed_model
omicverse.metabol.msea_gsea
omicverse.metabol.msea_ora
omicverse.metabol.mummichog_basic
omicverse.metabol.normalize
omicverse.metabol.opls_da
omicverse.metabol.parse_lipid
omicverse.metabol.pathway_bar
omicverse.metabol.pathway_dot
omicverse.metabol.plsda
omicverse.metabol.pyMetabo
omicverse.metabol.read_lcms
omicverse.metabol.read_metaboanalyst
omicverse.metabol.read_wide
omicverse.metabol.roc_feature
omicverse.metabol.run_mofa
omicverse.metabol.s_plot
omicverse.metabol.sample_qc
omicverse.metabol.sample_qc_plot
omicverse.metabol.serrf
omicverse.metabol.transform
omicverse.metabol.vip_bar
omicverse.metabol.volcano
omicverse.micro.Alpha
omicverse.micro.attach_tree
omicverse.micro.Beta
omicverse.micro.clr
omicverse.micro.collapse_taxa
omicverse.micro.combine_studies
omicverse.micro.DA
omicverse.micro.fetch_franzosa_ibd_2019
omicverse.micro.filter_by_prevalence
omicverse.micro.ilr
omicverse.micro.meta_da
omicverse.micro.MMvec
omicverse.micro.Ordinate
omicverse.micro.paired_cca
omicverse.micro.paired_spearman
omicverse.micro.plot_embedding_biplot
omicverse.micro.plot_mmvec_training
omicverse.micro.rarefy
omicverse.micro.simulate_paired
omicverse.space.bin2cell
omicverse.space.Cal_Spatial_Net
omicverse.space.calculate_gene_signature
omicverse.space.CAST
omicverse.space.cellcharter
omicverse.space.CellLoc
omicverse.space.CellMap
omicverse.space.clusters
omicverse.space.create_communication_anndata
omicverse.space.crop_space_visium
omicverse.space.Deconvolution
omicverse.space.GASTON
omicverse.space.map_spatial_auto
omicverse.space.map_spatial_manual
omicverse.space.merge_cluster
omicverse.space.moranI
omicverse.space.nmf_tissue_zones
omicverse.space.pySpaceFlow
omicverse.space.pySTAGATE
omicverse.space.pySTAligner
omicverse.space.read_visium_10x
omicverse.space.rotate_space_visium
omicverse.space.salvage_secondary_labels
omicverse.space.spatial_autocorr
omicverse.space.spatial_neighbors
omicverse.space.STT
omicverse.space.svg
omicverse.space.sync_visium_hd_seg_geometries
omicverse.space.Tangram
omicverse.space.update_classification_from_database
omicverse.space.visium_10x_hd_cellpose_expand
omicverse.space.visium_10x_hd_cellpose_gex
omicverse.space.visium_10x_hd_cellpose_he
omicverse.bulk2single.Bulk2Single
omicverse.bulk2single.bulk2single_plot_cellprop
omicverse.bulk2single.bulk2single_plot_correlation
omicverse.bulk2single.BulkTrajBlend
omicverse.bulk2single.Single2Spatial
omicverse.pl.add_density_contour
omicverse.pl.add_palue
omicverse.pl.add_pie2spatial
omicverse.pl.add_streamplot
omicverse.pl.branch_streamplot
omicverse.pl.bardotplot
omicverse.pl.boxplot
omicverse.pl.branch_streamplot
omicverse.pl.calculate_gene_density
omicverse.pl.ccc_heatmap
omicverse.pl.ccc_network_plot
omicverse.pl.ccc_stat_plot
omicverse.pl.cell_cor_heatmap
omicverse.pl.CellChatViz
omicverse.pl.cellproportion
omicverse.pl.complexheatmap
omicverse.pl.contour
omicverse.pl.ConvexHull
omicverse.pl.create_custom_colormap
omicverse.pl.dotplot
omicverse.pl.dynamic_heatmap
omicverse.pl.dynamic_trends
omicverse.pl.embedding
omicverse.pl.embedding_adjust
omicverse.pl.embedding_atlas
omicverse.pl.embedding_celltype
omicverse.pl.embedding_density
omicverse.pl.feature_heatmap
omicverse.pl.ForbiddenCity
omicverse.pl.gen_mpl_labels
omicverse.pl.geneset_wordcloud
omicverse.pl.group_heatmap
omicverse.pl.marker_heatmap
omicverse.pl.markers_dotplot
omicverse.pl.palette
omicverse.pl.plot1cell
omicverse.pl.plot_cellproportion
omicverse.pl.plot_embedding_celltype
omicverse.pl.plot_flowsig_network
omicverse.pl.plot_grouped_fractions
omicverse.pl.plot_pca_variance_ratio
omicverse.pl.plot_set
omicverse.pl.plot_spatial
omicverse.pl.plot_text_set
omicverse.pl.rank_genes_groups_dotplot
omicverse.pl.single_group_boxplot
omicverse.pl.tsne
omicverse.pl.umap
omicverse.pl.venn
omicverse.pl.violin
omicverse.pl.volcano
omicverse.datasets.bhattacherjee
omicverse.datasets.blobs
omicverse.datasets.bm
omicverse.datasets.bone_marrow
omicverse.datasets.burczynski06
omicverse.datasets.chromaffin
omicverse.datasets.cite_seq
omicverse.datasets.create_mock_dataset
omicverse.datasets.decov_bulk_covid_bulk
omicverse.datasets.decov_bulk_covid_single
omicverse.datasets.dentate_gyrus
omicverse.datasets.dentate_gyrus_scvelo
omicverse.datasets.download_data
omicverse.datasets.download_data_requests
omicverse.datasets.get_adata
omicverse.datasets.gillespie
omicverse.datasets.haber
omicverse.datasets.hematopoiesis
omicverse.datasets.hematopoiesis_raw
omicverse.datasets.hg_forebrain_glutamatergic
omicverse.datasets.hl60
omicverse.datasets.human_tfs
omicverse.datasets.krumsiek11
omicverse.datasets.moignard15
omicverse.datasets.multi_brain_5k
omicverse.datasets.nascseq
omicverse.datasets.pancreas_cellrank
omicverse.datasets.pancreatic_endocrinogenesis
omicverse.datasets.paul15
omicverse.datasets.pbmc3k
omicverse.datasets.pbmc8k
omicverse.datasets.sc_ref_Lymph_Node
omicverse.datasets.sceu_seq_organoid
omicverse.datasets.sceu_seq_rpe1
omicverse.datasets.scifate
omicverse.datasets.scnt_seq_neuron_labeling
omicverse.datasets.scnt_seq_neuron_splicing
omicverse.datasets.scslamseq
omicverse.datasets.seqfish
omicverse.datasets.toggleswitch
omicverse.datasets.zebrafish
omicverse.external.GraphST
omicverse.utils.biocontext.call_tool
omicverse.utils.biocontext.get_ensembl_id
omicverse.utils.biocontext.get_fulltext
omicverse.utils.biocontext.get_uniprot_id
omicverse.utils.biocontext.list_tools
omicverse.utils.biocontext.query_alphafold
omicverse.utils.biocontext.query_cell_ontology
omicverse.utils.biocontext.query_chebi
omicverse.utils.biocontext.query_efo
omicverse.utils.biocontext.query_go
omicverse.utils.biocontext.query_hpa
omicverse.utils.biocontext.query_interpro
omicverse.utils.biocontext.query_opentargets
omicverse.utils.biocontext.query_panglaodb
omicverse.utils.biocontext.query_reactome
omicverse.utils.biocontext.query_string
omicverse.utils.biocontext.query_uniprot
omicverse.utils.biocontext.search_clinical_trials
omicverse.utils.biocontext.search_drugs
omicverse.utils.biocontext.search_interpro
omicverse.utils.biocontext.search_literature
omicverse.utils.biocontext.search_preprints
omicverse.utils.biocontext.search_pride
omicverse.utils.cal_paga
omicverse.utils.cluster
omicverse.utils.convert2gene_id
omicverse.utils.convert2gene_symbol
omicverse.utils.convert2symbol
omicverse.utils.convert_adata_for_rust
omicverse.utils.convert_to_pandas
omicverse.utils.download_CaDRReS_model
omicverse.utils.download_GDSC_data
omicverse.utils.download_geneid_annotation_pair
omicverse.utils.download_pathway_database
omicverse.utils.download_tosica_gmt
omicverse.utils.geneset_prepare
omicverse.utils.get_gene_annotation
omicverse.utils.gtf_to_pair_tsv
omicverse.utils.LDA_topic
omicverse.utils.load_metabolights
omicverse.utils.mde
omicverse.utils.plot_paga
omicverse.utils.refine_label
omicverse.utils.retrieve_layers
omicverse.utils.roe
omicverse.utils.store_layers
omicverse.utils.symbol2id
omicverse.utils.weighted_knn_trainer
omicverse.utils.weighted_knn_transfer
omicverse.utils.wrap_dataframe
Release Notes
Developer guild
Registered Functions — GPU Support Overview
Discussion
GitHub
Repository
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omicverse.external.GraphST
omicverse.external.GraphST
#
# Author: Yahui Long # File Name: __init__.py # Description:
