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OmicVerse Documentation
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<li class="toctree-l1"><a class="reference internal" href="Installation_guild.html">OmicVerse Installation Guide</a></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="tutorials/index.html">Tutorials</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_genetics.html">Genomics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-genetics/t_genetics_01_gwas_pipeline.html">GWAS pipeline 1 — From genotypes to a fine-mapped locus</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-genetics/t_genetics_02_functional_followup.html">GWAS pipeline 2 — From a GWAS hit to a mechanism</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-genetics/t_genetics_03_spatially_resolved_gwas.html">GWAS pipeline 3 — Spatially Resolved GWAS Mapping</a></li>
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<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_bulk.html">Bulk Transcriptomics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_bulk_upstream.html">Upstream</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_mapping_STAR.html">Bulk RNA-seq mapping with STAR</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_mapping_kbpython.html">Bulk RNA-seq mapping with kb-python</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_bulk_preprocessing.html">Preprocessing</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_bulk_combat.html">Batch correction in Bulk RNA-seq or microarray data</a></li>
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<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_bulk_downstream.html">Downstream</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_deg.html">Different Expression Analysis</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_deseq2.html">Different Expression Analysis with DEseq2</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_timecourse.html">Bulk RNA-seq time-course analysis</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_network.html">Protein-Protein interaction (PPI) analysis by String-db</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_wgcna.html">WGCNA (Weighted gene co-expression network analysis) analysis</a></li>
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<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_bulk_deconvolution.html">Deconvolution</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_decov_bulk.html">Bulk deconvolution with reference scRNA-seq</a></li>
</ul>
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<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_bulk_others.html">Others</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-bulk/t_tcga.html">TCGA database preprocess</a></li>
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</ul>
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<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_single.html">Single-Cell Transcriptomics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_alignment.html">Alignment</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_alignment_1k.html">Alignment and analysis of single-cell RNA-seq data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_alignment_kb.html">scRNA-seq preprocessing with kb-python (kallisto | bustools)</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_alignment_compare.html">Benchmarking the simpleaf and kb-python alignment backends</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_alignment_velocity.html">Alignment and RNA velocity analysis of single-cell RNA-seq data.</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_preprocessing.html">Preprocessing</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_preprocess_cpu.html">Preprocessing the data of scRNA-seq with omicverse[CPU-GPU-mixed]</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_preprocess_gpu.html">Preprocessing the data of scRNA-seq with omicverse[GPU]</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_preprocess_rust.html">Preprocessing the data of scRNA-seq [Rust / out-of-memory]</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_ambient_rna.html">Removing ambient / contamination RNA from droplet scRNA-seq</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_cluster.html">Clustering space</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_cnmf.html">GeneModule Identified</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_lazy.html">Lazy analysis of scRNA-seq</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_batch.html">Batch correction</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/batch/index.html">Batch correction and data integration</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/batch/t_single_batch.html">Data integration and batch correction</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/batch/zoo/index.html">Batch-correction — backend zoo</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_annotation.html">Annotation</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_anno_noref.html">Reference-free automated single-cell cell type annotation</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_anno_ref.html">Reference automated single-cell cell type annotation</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_cellvote.html">Consensus annotation with CellVote — PBMC3k</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_cellmatch.html">Mapping Cell Names to the Cell Ontology/Taxonomy</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/anno-zoo/index.html">Individual methods</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_metacell.html">MetaCell</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/index.html">MetaCell</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/t_metacell_recommended.html">Recommended workflow: SEACells end-to-end + downstream sanity</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/t_metacell_multisample.html">Multi-sample metacells with batch correction</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/index.html">MetaCell zoo</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/t_metacell_seacells.html">SEACells — kernel archetypal analysis</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/t_metacell_metaq.html">MetaQ — VQ-VAE codebook metacells</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/t_metacell_supercell.html">SuperCell — kNN graph + walktrap community detection</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/t_metacell_kmeans.html">k-means — the trivial baseline that’s often hard to beat</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/t_metacell_random.html">random — the honest lower-bound baseline</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/t_metacell_geosketch.html">GeoSketch — density-aware sketching as a metacell baseline</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/metacell/zoo/t_metacell_compare.html">Side-by-side comparison of all metacell backends</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_trajectory.html">Trajectory</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/trajectory/index.html">Trajectory inference</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/trajectory/t_traj_slingshot.html">Trajectory Inference with Slingshot</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/trajectory/t_traj_fate.html">Unified terminal-state & fate-probability inference</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/trajectory/zoo/index.html">Trajectory inference — backend zoo</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_cellfate_gene.html">Timing-associated genes analysis with TimeFateKernel</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_cellfate.html">Identify the driver regulators of cell fate decisions</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_perturb.html">In-silico Perturbation</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/perturb/index.html">In-silico gene perturbation</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/perturb/t_perturb_sctenifoldknk.html">In-silico perturbation with scTenifoldKnk (<code class="docutils literal notranslate"><span class="pre">backend='sctenifoldknk'</span></code>)</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/perturb/t_perturb_celloracle.html">In-silico perturbation with CellOracle (<code class="docutils literal notranslate"><span class="pre">backend='cell_oracle'</span></code>)</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/perturb/t_perturb_unified.html">Unified downstream analysis for <code class="docutils literal notranslate"><span class="pre">ov.single.perturb</span></code></a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_communication.html">Cell-Cell Communication</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_ccc_cellphonedb.html">Cell-cell communication analysis with CellPhoneDB</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_ccc_liana.html">Cell-cell communication analysis with LIANA+</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_cell_structure.html">Cell Structure</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_deg_single.html">Differential expression and celltype analysis [All Cell]</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_scdeg.html">Differential expression analysis [Meta Cell]</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_scenic.html">Gene Regulatory Network Analysis with SCENIC</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_scdrug.html">Drug response predict with scDrug</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_simba.html">Data integration and batch correction with SIMBA</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_cnv.html">Copy-Number Variation</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_copykat.html">Single-cell copy-number variation with CopyKAT</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_infercnv.html">Single-cell copy-number variation with inferCNV</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_metabolism.html">Metabolism</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_metabolism.html">Single-cell metabolic landscape of a head & neck tumour</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_metabolism_ccc.html">Metabolite cell-cell communication in a tumour microenvironment</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_enrichment.html">Enrichment</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_aucell.html">Pathway analysis with AUCell</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/enrichment/t_es_compare.html">Comparing enrichment-score methods on scRNA-seq</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_velocity.html">Velocity</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-velo/t_velo.html">Velocity Basic Calculation</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-velo/t_graphvelo.html">Velocity Optimization</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-velo/t_regvelo.html">RNA velocity and regulatory perturbation analysis with RegVelo</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-velo/t_regvelo_infer_grn.html">Run RegVelo with inferred GRN</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-velo/t_velo_cellrank.html">Velocity-guided CellRank Analysis</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_multi_omics.html">Multi-omics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_mofa.html">Multi omics analysis by MOFA</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_mofa_glue.html">Multi omics analysis by MOFA and GLUE</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_anno_trans.html">Celltype annotation transfer in multi-omics</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_single_ev.html">Single-EV proteomics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-single/t_single_ev.html">Single-extracellular-vesicle (single-EV) proteomics</a></li>
</ul>
</details></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_spatial.html">Spatial Transcriptomics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_spatial_spata2.html">SPATA2-inspired utilities</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_spata2py.html">SPATA2-inspired AnnData spatial utilities in OmicVerse</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_spatial_preprocessing.html">Preprocessing</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_crop_rotate.html">Crop and Rotation of spatial transcriptomic data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_cellpose.html">Cell Segmentation (10x HD)</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_nanostring_preprocess.html">Analyze NanoString data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_xenium_preprocess.html">Analyze Xenium data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_atera_preprocess.html">Analyze 10x Atera (WTA Preview) FFPE breast cancer data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_visium_hd_preprocess.html">Analyze Visium HD data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_staligner.html">Spatial integration and clustering</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_spatial_clustering.html">Clustering</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/cluster/t_cluster_graphst.html">Spatial clustering with GraphST + pymclustR</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/cluster/t_cluster_binary.html">Spatial clustering with BINARY + pymclustR</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/cluster/t_cluster_stagate.html">Spatial clustering with STAGATE + pymclustR</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/cluster/t_cluster_cast.html">Spatial clustering with CAST + pymclustR</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/cluster/t_cluster_banksy.html">Spatial clustering with BANKSY + pymclustR</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_spatial_deconvolution.html">Deconvolution</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_spaceflow.html">Identifying Pseudo-Spatial Map</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_decov.html">Spatial deconvolution with reference scRNA-seq</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_decov_rctd.html">Spatial deconvolution with RCTD</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_flashdeconv.html">FlashDeconv: Fast Spatial Deconvolution via Structure-Preserving Sketching</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_starfysh_new.html">Spatial deconvolution without reference scRNA-seq</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_spatial_he_zoo.html">H&E → spatial transcriptomics prediction (HE-zoo)</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/he-zoo/t_histo_hest_fm.html">HEST-FM — pathology foundation model + ridge head</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/he-zoo/t_histo_stpath.html">STPath — zero-shot generative foundation model</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/he-zoo/t_histo_stflow.html">STFlow — per-slide flow-matching denoiser</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/he-zoo/t_histo_istar.html">iStar — super-resolve a paired Visium + H&E sample</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_spatial_downstream.html">Downstream</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_stt.html">Spatial transition tensor of single cells</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_commot_flowsig.html">Spatial Communication</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_gaston.html">Spatial IsoDepth Calculation</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-space/t_slat.html">Single cell spatial alignment tools</a></li>
</ul>
</details></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_airr.html">Immune Repertoire</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-airr/t_airr_01_singlecell.html">Single-cell TCR + transcriptome — the immune-repertoire pipeline</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-airr/t_airr_02_bulk.html">Bulk TCR immune-repertoire analysis with <code class="docutils literal notranslate"><span class="pre">ov.airr</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-airr/t_airr_03_bcr.html">B-cell receptor repertoire analysis with <code class="docutils literal notranslate"><span class="pre">ov.airr</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-airr/t_airr_06_bcr_singlecell.html">Single-cell BCR + transcriptome — clonal expansion, isotypes and somatic hypermutation</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-airr/t_airr_04_tcr.html">TCR specificity analysis — grouping receptors by their antigen</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-airr/t_airr_05_tcr_gex.html">Joint single-cell TCR + gene-expression analysis — a CoNGA-style workflow</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_flow.html">Flow Cytometry</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-flow/t_flow_01_reading_and_compensation.html">Reading FCS, compensation and display scales</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-flow/t_flow_02_gating.html">Gates, the gating strategy, and reading the numbers</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-flow/t_flow_03_gatingml.html">Saving a strategy and applying it to a batch (Gating-ML 2.0)</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-flow/t_flow_04_flowsom.html">FlowSOM — and what clustering does not replace</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-flow/t_flow_05_real_data.html">The whole module on real data</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-flow/t_flow_06_case_study.html">Case study — immunophenotyping PBMC after cardiac arrest</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_protein.html">Proteomics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-protein/t_protein_01_bulk_pipeline.html">Bulk LC-MS/MS proteomics — the best-practice pipeline</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-protein/t_protein_02_missing_values.html">Missing values in proteomics — diagnosis & imputation</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-protein/t_protein_03_summarization_dia.html">Peptide → protein summarization & the DIA workflow</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-protein/t_protein_04_differential_expression.html">Differential expression in proteomics: a benchmark with ground truth</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-protein/t_protein_05_olink.html">Olink NPX — affinity proteomics analysis</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_mol.html">Structure, Docking & Dynamics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-mol/t_mol_structure.html">Protein structure of an omics target — fetch, visualize, and <em>assess before you trust</em></a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-mol/t_mol_druggability.html">Is the target druggable? — binding pockets and known drugs</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-mol/t_mol_docking.html">Molecular docking — <em>validate the protocol, then dock the candidate</em></a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-mol/t_mol_dynamics.html">Molecular dynamics — <em>from a static model to motion</em></a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_synbio.html">Synthetic Biology</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-synbio/t_synbio_01_intro.html">Synthetic biology with <code class="docutils literal notranslate"><span class="pre">ov.synbio</span></code> — from metabolism to enzyme to DNA</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-synbio/t_synbio_02_circuits_to_pathways.html">ov.synbio II — circuits, CRISPR, assembly & pathway design</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-synbio/t_synbio_03_crispr_library.html">ov.synbio III — CRISPR editing & directed-evolution libraries</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-synbio/t_synbio_04_advanced.html">ov.synbio IV — advanced SOTA: mRNA design, de-novo binders, prime editing</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-synbio/t_synbio_case01_succinate.html">Case study I — an <em>E. coli</em> succinate cell factory</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-synbio/t_synbio_case02_dhfr_engineering.html">Case study II — engineering a more thermostable DHFR</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-synbio/t_synbio_case03_dhfr_evaluation.html">Case study III — evaluating a protein design (does it get <em>better</em>?)</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_metabol.html">Metabolomics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_01_intro.html">Metabolomics preprocessing and univariate statistics</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_02_multivariate.html">Multivariate discrimination with PLS-DA and OPLS-DA</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_03_pathway.html">Metabolite-set enrichment analysis (MSEA)</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_04_untargeted.html">Untargeted LC-MS and mummichog pathway inference</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_05_lipidomics.html">Lipidomics — the <em>lipidr</em> workflow in omicverse</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_06_batch_correction.html">Batch effect and drift correction for LC-MS</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_07_multifactor.html">Multi-factor designs — ASCA and linear mixed models</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_08_biomarker.html">Biomarker discovery — univariate AUC + multivariate panel</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_09_dgca.html">Differential correlation — DGCA</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_10_multiomics.html">Multi-omics integration — metabolomics + RNA-seq with MOFA</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-metabol/t_metabol_11_real_data_mtbls1.html">Real-data case study — MTBLS1 (urine NMR, Type 2 Diabetes)</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_epigenetics.html">Epigenetics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_01_atac_preprocess.html">scATAC-seq preprocessing and quality control</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_02_atac_clustering_annotation.html">scATAC clustering, annotation and gene activity</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_03_atac_chromvar.html">Transcription-factor motif activity with chromVAR</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_04_peak_to_gene.html">Peak-to-gene linkage (multiome)</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_05_marker_peaks.html">Marker peaks and differential accessibility</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_06_integration_label_transfer.html">scRNA–scATAC integration and label transfer</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_07_bulk_hic.html">Bulk Hi-C — contact maps, compartments and TADs</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_08_single_cell_hic.html">Single-cell Hi-C — imputation and cell-cycle embedding</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_09_bulk_chipseq_upstream.html">Bulk ChIP-seq upstream: FASTQ → peaks</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-epigenetics/t_epi_10_bulk_footprinting.html">Bulk ATAC footprinting — TF activity from Tn5 cut profiles</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_microbiome.html">Microbiome</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-microbiome/t_16s_amplicon.html">16S rRNA amplicon analysis with OmicVerse</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-microbiome/t_16s_phylogeny.html">16S phylogeny: MAFFT → FastTree → Faith PD + UniFrac</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-microbiome/t_16s_dada2.html">DADA2 backend: pure-Python ASV inference</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-microbiome/t_16s_da_comparison.html">Differential abundance: Wilcoxon vs DESeq2 vs ANCOM-BC</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-microbiome/t_16s_meta_analysis.html">Cross-cohort 16S meta-analysis</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_multi_omics.html">Multi-Omics</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-Multi-Omics/bulk-single/t_bulktrajblend.html">Bulk RNA-seq generate ‘interrupted’ cells to interpolate scRNA-seq</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-Multi-Omics/bulk-single/t_bulk2single.html">Bulk RNA-seq to Single RNA-seq</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-Multi-Omics/bulk-single/t_single2spatial.html">Single RNA-seq to Spatial RNA-seq</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-Multi-Omics/micro-meta/t_micro_metabol_paired.html">Paired microbe ↔ metabolite integration (Franzosa 2019 IBD)</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_foundation.html">Foundation Models</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_foundation_overview.html">Overview</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="simple">
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_foundation_skill_ready.html">Skill-Ready Models</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-llm/t_scgpt.html">scGPT</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-llm/t_geneformer.html">GeneFormer</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-llm/t_uce.html">UCE</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-llm/t_scfoundation.html">scFoundation</a></li>
<li class="toctree-l4"><a class="reference internal" href="Tutorials-llm/t_cellplm.html">CellPLM</a></li>
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_foundation_core.html">Core Models</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="simple">
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_foundation_specialized.html">Specialized Models</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="simple">
</ul>
</details></li>
<li class="toctree-l3 has-children"><a class="reference internal" href="tutorials/index_foundation_domain.html">Domain-Specific Models</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="simple">
</ul>
</details></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="tutorials/index_plotting.html">Visualization</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_visualize_single.html">Visualization of single cell RNA-seq</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_visualize_bulk.html">Visualization of Bulk RNA-seq</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_palette.html">Palette optimization for publication-quality single-cell & spatial plots</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_publication_plotting.html">Scientific plotting for publication with OmicVerse</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_visualize_colorsystem.html">Color system</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_plot1cell.html">Circular UMAP with plot1cell</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_funkyheatmap.html">Funky heatmaps for benchmark / multi-metric tables</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_clinical_stats_layout.html">Clinical statistics and figure assembly</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-plotting/t_statistical_plots.html">Statistical plots from a table</a></li>
</ul>
</details></li>
</ul>
</details></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="omicclaw/index.html">OmicClaw</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2 has-children"><a class="reference internal" href="omicclaw/index_gateway.html">Gateway and Channels</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_msg_bot_overview.html">OmicClaw Gateway Overview</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_setup_auth.html">OmicClaw Setup and Auth</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_channel_telegram.html">OmicClaw Telegram Tutorial</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_channel_feishu.html">OmicClaw Feishu 教程</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_channel_imessage.html">OmicClaw iMessage Tutorial</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_channel_qq.html">OmicClaw QQ Tutorial</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_session_commands.html">OmicClaw Session Workflow</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-jarvis/t_troubleshooting.html">OmicClaw Troubleshooting</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="omicclaw/index_mcp.html">MCP Server</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_guide.html">OmicVerse MCP Server</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_quickstart.html">OmicVerse MCP Quick Start</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_full_start.html">OmicVerse MCP Full Start</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_tools.html">OmicVerse MCP Tool Catalog</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_clients.html">OmicVerse MCP Clients and Deployment</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_runtime.html">OmicVerse MCP Runtime and Troubleshooting</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_reference.html">OmicVerse MCP Reference</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_mcp_claude_code.html">Using OmicVerse MCP with Claude Code — Step by Step</a></li>
</ul>
</details></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="omicclaw/index_notebooks.html">General Notebooks</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/t_ov_agent_pbmc3k.html">J.A.R.V.I.S. with PBMC3k</a></li>
<li class="toctree-l3"><a class="reference internal" href="Tutorials-llm/ov_agent_ten_task_suite.html">J.A.R.V.I.S. with Ten-Task Suite</a></li>
</ul>
</details></li>
</ul>
</details></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="api/index.html">API Reference</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2 has-children"><a class="reference internal" href="api/user.html">User API</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.generate_reference_table.html">omicverse.generate_reference_table</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.settings.cpu_gpu_mixed_init.html">omicverse.settings.cpu_gpu_mixed_init</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.settings.gpu_init.html">omicverse.settings.gpu_init</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.load.html">omicverse.io.load</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read.html">omicverse.io.read</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_10x_h5.html">omicverse.io.read_10x_h5</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_10x_mtx.html">omicverse.io.read_10x_mtx</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_csv.html">omicverse.io.read_csv</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_h5ad.html">omicverse.io.read_h5ad</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_nanostring.html">omicverse.io.read_nanostring</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_visium_hd.html">omicverse.io.read_visium_hd</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_visium_hd_bin.html">omicverse.io.read_visium_hd_bin</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_visium_hd_seg.html">omicverse.io.read_visium_hd_seg</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.read_xenium.html">omicverse.io.read_xenium</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.save.html">omicverse.io.save</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.spatial.read_visium.html">omicverse.io.spatial.read_visium</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.io.spatial.write_visium_hd_cellseg.html">omicverse.io.spatial.write_visium_hd_cellseg</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.amplicon_16s_pipeline.html">omicverse.alignment.amplicon_16s_pipeline</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.build_amplicon_anndata.html">omicverse.alignment.build_amplicon_anndata</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.build_phylogeny.html">omicverse.alignment.build_phylogeny</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.bulk_rnaseq_pipeline.html">omicverse.alignment.bulk_rnaseq_pipeline</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.count.html">omicverse.alignment.count</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.cutadapt.html">omicverse.alignment.cutadapt</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.dada2_pipeline.html">omicverse.alignment.dada2_pipeline</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.dada2.denoise.html">omicverse.alignment.dada2.denoise</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.vsearch.dereplicate.html">omicverse.alignment.vsearch.dereplicate</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.fastp.html">omicverse.alignment.fastp</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.fasttree.html">omicverse.alignment.fasttree</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.featureCount.html">omicverse.alignment.featureCount</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.fetch_rdp.html">omicverse.alignment.fetch_rdp</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.fetch_silva.html">omicverse.alignment.fetch_silva</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.fetch_sintax_ref.html">omicverse.alignment.fetch_sintax_ref</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.dada2.filter_and_trim.html">omicverse.alignment.dada2.filter_and_trim</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.vsearch.filter_quality.html">omicverse.alignment.vsearch.filter_quality</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.fqdump.html">omicverse.alignment.fqdump</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.dada2.learn_errors.html">omicverse.alignment.dada2.learn_errors</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.mafft.html">omicverse.alignment.mafft</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.dada2.make_seqtab.html">omicverse.alignment.dada2.make_seqtab</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.dada2.merge_pairs.html">omicverse.alignment.dada2.merge_pairs</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.parallel_fastq_dump.html">omicverse.alignment.parallel_fastq_dump</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.prefetch.html">omicverse.alignment.prefetch</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/reference/omicverse.alignment.ref.html">omicverse.alignment.ref</a></li>
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