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OmicVerse 文档
OmicVerse 安装指南
教程
Bulk RNA-seq
使用STAR进行Bulk RNA-seq比对
使用kb-python进行Bulk RNA-seq比对
Bulk RNA-seq或微阵列数据中的批次校正
差异表达分析
使用DEseq2进行差异表达分析
使用String-db进行蛋白质-蛋白质相互作用（PPI）分析
WGCNA（加权基因共表达网络分析）分析
基于参考scRNA-seq的Bulk反卷积
TCGA数据库预处理
单细胞 RNA-seq
单细胞RNA-seq数据的比对和分析
单细胞RNA-seq数据的比对和RNA速度分析
Preprocessing the data of scRNA-seq with omicverse[CPU-GPU-mixed]
Preprocessing the data of scRNA-seq with omicverse[GPU]
单细胞聚类和注释
Data integration and batch correction
cNMF：共识非负矩阵分解
单细胞RNA-seq懒惰分析
无参考自动化单细胞细胞类型注释
使用参考的自动化单细胞细胞类型注释
Mapping Cell Names to the Cell Ontology/Taxonomy
单独的注释方法
使用 SCSA 进行细胞类型自动注释
Automatic cell type annotation with GPT/Other
使用 MetaTiME 的细胞类型自动注释
Using scMulan to annotate cell types in Heart, Lung, Liver, Bone marrow, Blood, Brain, and Thymus
Celltype annotation migration(mapping) with TOSICA
CytoTRACE：细胞轨迹重建和推理
使用 Diffusion Map 和 PAGA 进行轨迹推断
使用 Slingshot 进行轨迹推断
使用 Palantir 进行轨迹推断
使用 scTour 进行轨迹推断
使用 Monocle 2 进行轨迹推断
使用 StaVIA 进行轨迹推断
使用 StaVIA 进行轨迹推断：toy_multifurcating 官方测试数据
使用 VIA 进行轨迹推断
Trajectory Inference with VIA and scVelo
Timing-associated genes analysis with TimeFateKernel
Identify the driver regulators of cell fate decisions
单细胞差异表达分析
Differential expression analysis [Meta Cell]
Gene Regulatory Network Analysis with SCENIC
Drug response predict with scDrug
Data integration and batch correction with SIMBA
Single-cell copy-number variation with CopyKAT
Single-cell copy-number variation with inferCNV
Pathway analysis with AUCell
Comparing enrichment-score methods on scRNA-seq
使用 CellPhoneDB 进行细胞通讯分析
使用 LIANA+ 进行细胞通讯分析
Velocity Basic Calculation
Velocity Optimization
使用 RegVelo 进行 RNA velocity 和调控扰动分析
使用推断 GRN 运行 RegVelo
基于 RNA velocity 的 CellRank 分析
Multi omics analysis by MOFA
Multi omics analysis by MOFA and GLUE
转录组数据转移和细胞类型注释
Bulk 转单细胞与跨平台
Bulk RNA-seq generate ‘interrupted’ cells to interpolate scRNA-seq
批量 RNA-seq 到单细胞 RNA-seqBulk2Single 用于批量 RNA-seq 反卷积。我们从 Bulk2Space 算法中提取了 beta-VAE 部分，并构建了一种可以从批量 RNA-seq 反卷积到单细胞 RNA-seq 的算法。此外，我们重新设计了数据的输入和输出，使其更兼容 Python 环境中的分析约定。Paper: De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolutionCode: https://github.com/ZJUFanLab/bulk2spaceColab_Reproducibility：https://colab.research.google.com/drive/1He71hAyeAv1DHQyXUlxtoJ4QvwZwW7I0?usp=sharing本教程介绍了如何从批量 RNA-seq 和参考 scRNA-seq 数据中读取、设置和训练模型。我们使用 pdac 数据集作为示例
Single RNA-seq to Spatial RNA-seq
空间转录组学
裁剪和旋转空间转录组学数据
细胞分割（10x HD）
分析 NanoString 数据
Analyze 10x Atera (WTA Preview) FFPE breast cancer data
分析 Visium HD 数据
空间聚类和降噪表达
空间集成和聚类
识别伪空间映射
带参考 scRNA-seq 的空间反卷积
Spatial deconvolution with RCTD
FlashDeconv：通过结构保留草图实现快速空间反卷积
不使用参考 scRNA-seq 的空间反卷积
单细胞空间转移张量
Spatial CommunicationSpatial communication is a point of interest for us for the 空间转录组学 Society, and we would like to find the conduction process of spatial communication.Here, we introduce two method integrated in OmicVerse named
COMMOT
and
flowsig
.We made three improvements in integrating the
COMMOT
and
flowsig
algorithm in OmicVerse:- We reduced the installation conflict of
COMMOT
and
flowsig
, user only need to update OmicVerse to the latest version.- We optimized the 可视化 of
COMMOT
and
flowsig
and unified the data 预处理 process so that users don’t need to struggle with different data processing flows.- We have fixed some bugs that could occur during function.If you found this tutorial helpful, please cite
COMMOT
,
flowsig
and OmicVerse:- Cang, Z., Zhao, Y., Almet, A.A. et al. Screening cell–cell communication in 空间转录组学 via collective optimal transport. Nat Methods 20, 218–228 (2023). https://doi.org/10.1038/s41592-022-01728-4- Almet, A.A., Tsai, YC., Watanabe, M. et al. Inferring pattern-driving intercellular flows from 单细胞 and 空间转录组学. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02380-w
空间同深度计算
单细胞空间对齐工具
基础模型
ov.fm — 基础模型模块
ov.fm — Unified Foundation Model API
scGPT
scGPT
Geneformer
GeneFormer
UCE
UCE
scFoundation
scFoundation
CellPLM
CellPLM
scBERT
scBERT — 基础模型教程
GeneCompass
GeneCompass — Foundation Model Tutorial
Nicheformer
Nicheformer — 基础模型教程
scMulan
scMulan — 基础模型教程
tGPT
tGPT — Foundation Model Tutorial
CellFM
CellFM — Foundation Model Tutorial
scCello
scCello — 基础模型教程
scPRINT
scPRINT — 基础模型教程
AIDO.Cell
AIDO.Cell — 基础模型教程
PULSAR
PULSAR — Foundation Model Tutorial
Tabula
Tabula — 基础模型教程
ATACformer
ATACformer — Foundation Model Tutorial
scPlantLLM
scPlantLLM — 基础模型教程
LangCell
LangCell — 基础模型教程
Cell2Sentence
Cell2Sentence — Foundation Model Tutorial
GenePT
GenePT — 基础模型教程
ChatCell
ChatCell — Foundation Model Tutorial
可视化与绘图
Visualization of single cell RNA-seq
批量 RNA-seq 的可视化在这一部分中，我们将介绍
omicverse
特殊绘图的教程。
Palette optimization for publication-quality single-cell & spatial plots
Color system
Circular UMAP with plot1cell
OmicClaw
网关与频道
OmicClaw Gateway 概述
OmicClaw 配置与认证
OmicClaw Telegram 教程
OmicClaw 飞书 教程
OmicClaw iMessage 教程
OmicClaw QQ 教程
OmicClaw 会话工作流程
OmicClaw 故障排查
MCP 服务器
OmicVerse MCP 服务器
OmicVerse MCP 快速开始
OmicVerse MCP 完整启动
OmicVerse MCP 工具目录
OmicVerse MCP 客户端与部署
OmicVerse MCP 运行时与故障排查
OmicVerse MCP 参考文档
在 Claude Code 中使用 OmicVerse MCP — 逐步指南
通用 Notebook
J.A.R.V.I.S. 与 PBMC3k
J.A.R.V.I.S. 十任务套件
API 参考
用户 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.hematopoiesis
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.pyVIA
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.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
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omicverse.datasets.scslamseq
目录
scslamseq()
omicverse.datasets.scslamseq
#
omicverse.datasets.
scslamseq
(
)
[源代码]
#
TODO: add data here
目录
scslamseq()
