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A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
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- __init__.py
- __init__.py
- _bcr.py
- _bulk.py
- _clonotype.py
- _metrics.py
- _qc.py
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- _tcr_gex.py
- io.py
- plotting.py
- __init__.py
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- kb_api.py
- mafft.py
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- phylogeny.py
- pipeline.py
- prefetch.py
- sanger.py
- simpleaf.py
- STAR.py
- vsearch.py
- __init__.py
- __init__.py
- _chm13.py
- _combat.py
- _decov.py
- _Deseq2.py
- _df_apply.py
- _dynamicTree.py
- _enrich_plot.py
- _Enrichment.py
- _Gene_module.py
- _gsea_numpy.py
- _network.py
- _ora.py
- _tcga.py
- _wgcna.py
- __init__.py
- _bulk2single.py
- _bulkdeconvolve.py
- _bulktrajblend.py
- _map_utils.py
- _map_utils1.py
- _scsemi.py
- _single2spatial.py
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- _vae.py
- allTFs_human.txt
- allTFs_mouse.txt
- allTFs_zebrafish.txt
- cellchat_interactions_and_tfs_human.csv
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- apoptosis_human.gmt
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- c2.cp.v7.5.1.symbols.gmt
- cell_cycle_human.gmt
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- features_model_training_17.csv
- gender_human.gmt
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- h.all.v7.5.1.symbols.gmt
- human_alias_list.txt
- human_lung.gmt
- human_t_cell_markers.gmt
- mart_export.txt
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- README.md
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- smoothDatakNN.py
- __init__.py
- _airr.py
- _ambient.py
- _crossspecies.py
- _cytometry.py
- _datasets.py
- _ev.py
- _flow.py
- _genetics.py
- _metabolism.py
- _protein.py
- _signatures.py
- _spatial.py
- _timecourse.py
- __init__.py
- _utils.py
- bulk.py
- data.py
- datasets.py
- io.py
- pl.py
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- single.py
- tl.py
- upstream.py
- utils.py
- __init__.py
- _aucell.py
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- _decouple.py
- _engine.py
- _gsea.py
- _gsva.py
- _mdt.py
- _method.py
- _methods.py
- _mlm.py
- _net.py
- _odeps.py
- _ora.py
- _pv.py
- _query_set.py
- _run.py
- _ucell.py
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- _viper.py
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- _zscore.py
- __init__.py
- bin2cell.py
- __init__.py
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- utils.py
- deconvolution.py
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- __init__.py
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- references.py
- run.py
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- __init__.py
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- hamster_to_human_gene.txt
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- singlecell_process.py
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- __init__.py
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- __init__.py
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- main.py
- utils.py
- visualize.py
- __init__.py
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- __init__.py
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- __init__.py
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- __init__.py
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- __init__.py
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- isodepth_scaling.py
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- parse_adata.py
- plot_cell_types.py
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- process_NN_output.py
- restrict_spots.py
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- __init__.py
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- __init__.py
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- preprocess.py
- readme.txt
- utils.py
- __init__.py
- gam.py
- graph_velocity.py
- kernel_density_smooth.py
- metrics.py
- mo.py
- plot.py
- tangent_space.py
- utils.py
- __init__.py
- adjacency_matrix.py
- model.py
- train.py
- report_template.html
- __init__.py
- _config.py
- _jackknife.py
- _manhattan_plot.py
- _regression_read.py
- _style.py
- _visualize.py
- cauchy_combination.py
- diagnosis.py
- find_latent_representation.py
- generate_ldscore.py
- latent_to_gene.py
- report.py
- spatial_ldsc.py
- __init__.py
- attribute_parsing.py
- create_missing_features.py
- parsing_error.py
- read_gtf.py
- __init__.py
- _harmony_cpu.py
- _harmony_mlx.py
- harmony.py
- lisi.py
- __init__.py
- bernoulli_model.py
- danb_model.py
- hotspot.py
- knn.py
- local_stats.py
- local_stats_pairs.py
- modules.py
- none_model.py
- normal_model.py
- plots.py
- sim_data.py
- utils.py
- .gitignore
- __init__.py
- aggregate_imputed.py
- cluster.py
- connected_components.py
- differential.py
- download_checkpoints.sh
- download_demo.sh
- enrich.py
- extract_features.py
- get_mask.py
- hipt_4k.py
- hipt_heatmap_utils.py
- hipt_model_utils.py
- image.py
- impute.py
- impute_by_basic.py
- LICENSE
- marker_score.py
- NOTICE.md
- pixannot.py
- plot_imputed.py
- plot_spots.py
- preprocess.py
- README.md
- reduce_dim.py
- reorganize_imputed.py
- requirements.txt
- rescale.py
- run.sh
- run_demo.sh
- select_genes.py
- structural_similarity.py
- train.py
- utils.py
- vision_transformer.py
- vision_transformer4k.py
- visual.py
- __init__.py
- metrics.py
- run_metric.py
- __init__.py
- annot_vae_model.py
- atac_reg_model.py
- gclayer.py
- modules.py
- refine_model.py
- vae_model.py
- velocity_field.py
- __init__.py
- metrics.py
- scatter_stream.py
- __init__.py
- batch_correction.py
- cell_trajectories.py
- check_velocity.py
- trad_velocity.py
- __init__.py
- anvi_dataloader.py
- anvi_dataloader_nogcn.py
- atac_dataloader.py
- collate.py
- dataloader.py
- dataloader_nogcn.py
- dataloader_utils.py
- ev.py
- output_results.py
- path_regularization.py
- pl.py
- tl.py
- train.py
- trainer.py
- trainer_anvi.py
- trainer_anvi_nogcn.py
- trainer_atac.py
- trainer_nogcn.py
- utils.py
- velocity_genes.py
- __init__.py
- rigor.py
- hmdb_blood_metabolite_concentration.tsv
- human_mouse_homology_gene_pair.csv
- metabolite_annotation_HMDB_summary.tsv
- human_met_sensor_update_Oct21_2025.tsv
- metabolite_associated_gene_reaction_HMDB_summary.tsv
- metabolite_associated_gene_reaction_HMDB_summary_mouse.tsv
- mouse_met_sensor_update_Oct21_2025.tsv
- __init__.py
- crosstalk_calculator.py
- crosstalk_diff.py
- crosstalk_plots.py
- fba_handler.py
- mebocost.py
- MetEstimator.py
- __init__.py
- data_utils.py
- engine.py
- LICENSE
- model.py
- __init__.py
- build_model.py
- init_model.py
- save_model.py
- train_model.py
- utils.py
- __init__.py
- basic_distributions.py
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- multivariate_gaussian.py
- poisson.py
- univariate_gaussian.py
- __init__.py
- Alpha_nodes.py
- basic_nodes.py
- Kc_node.py
- Kg_node.py
- multiview_nodes.py
- nongaussian_nodes.py
- Sigma_node.py
- Tau_nodes.py
- Theta_nodes.py
- U_nodes.py
- variational_nodes.py
- W_nodes.py
- Y_nodes.py
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- Z_nodes_GP.py
- Z_nodes_GP_mv.py
- ZgU_node.py
- __init__.py
- BayesNet.py
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- __init__.py
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- __init__.py
- config.py
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- __init__.py
- clustering.py
- core.py
- ddrtree.py
- differential.py
- dimension_reduction.py
- ordering.py
- plotting.py
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- __init__.py
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- __init__.py
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- __init__.py
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- __init__.py
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- A.pdb
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- __init__.py
- LICENSE
- pdbfixer.py
- soft.xml
- __init__.py
- _base_algorithm.py
- _bbknn.py
- _celltypist.py
- _harmony.py
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- __init__.py
- _get_metrics.py
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- annotation.py
- preprocessing.py
- visualization.py
- __init__.py
- calculate_PI.py
- layers.py
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- plot.py
- PROST.py
- utils.py
- KEGG_metabolism_nc.gmt
- REACTOME_metabolism.gmt
- __init__.py
- compute.py
- methods.py
- visualize.py
- __init__.py
- core.py
- LICENSE
- __init__.py
- common.py
- database.py
- download_cache.py
- ensembl_release.py
- ensembl_url_templates.py
- ensembl_versions.py
- exon.py
- fasta.py
- gene.py
- genome.py
- locus.py
- locus_with_genome.py
- logging.conf
- normalization.py
- reference_name.py
- search.py
- sequence_data.py
- serializable.py
- shell.py
- species.py
- transcript.py
- version.py
- __init__.py
- fit.py
- LICENSE
- _version.py
- binarization.py
- diptest.py
- export.py
- featureseq.py
- log.py
- math.py
- plotting.py
- prune.py
- rss.py
- transform.py
- utils.py
- __init__.py
- comparison.py
- geneExp.py
- utils.py
- wgcna.py
- __init__.py
- gui.py
- utilities.py
- __init__.py
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- __init__.py
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- __init__.py
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- __init__.py
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- contrastive_loss.py
- cosface_loss.py
- cross_batch_memory.py
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- generic_pair_loss.py
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- multi_similarity_loss.py
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- __init__.py
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- base_reducer.py
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- do_nothing_reducer.py
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- threshold_reducer.py
- __init__.py
- base_tester.py
- global_embedding_space.py
- global_twostream_embedding_space.py
- with_same_parent_label.py
- __init__.py
- accuracy_calculator.py
- common_functions.py
- distributed.py
- inference.py
- logging_presets.py
- loss_and_miner_utils.py
- loss_tracker.py
- module_with_records.py
- module_with_records_and_reducer.py
- stat_utils.py
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- transformations.py
- __init__.py
- _run.py
- _train_saturn.py
- LICENSE
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- requirements.txt
- saturn_multiple_seeds.py
- score_adata.py
- __init__.py
- scanorama.py
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- test_session_facade.py
- test_settings_mixed_devices.py
- test_skill_instruction_formatter.py
- test_smart_agent.py
- test_subagent_override_plumbing.py
- test_subagent_profile_schema.py
- test_tool_registry.py
- test_tool_runtime_handlers.py
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- test_turn_controller_execute_code_debug_output.py
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- test_versions.py
- __init__.py
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- test_llm_skill_selector.py
- test_notebook_task_extractor.py
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- test_skill_description_quality.py
- __init__.py
- _bare_sim.py
- conftest.py
- metabol_r_reference_driver.R
- test_augur.py
- test_bayesprism_thetapost.py
- test_cellvote_pbmc3k.py
- test_claw_cli.py
- test_cli_dispatch.py
- test_doubletfinder_qc.py
- test_enrichment_logp.py
- test_es_methods.py
- test_gateway_inprocess_channel_manager.py
- test_gpuex_scipy_rankdata.py
- test_histo_e2e.py
- test_homology_search.py
- test_io_atera.py
- test_io_facade_reexports.py
- test_io_fcs.py
- test_io_xenium_morphology.py
- test_metabol.py
- test_metabol_batch_corr.py
- test_metabol_fetchers.py
- test_metabol_multifactor.py
- test_metabol_qc.py
- test_metabol_r_parity.py
- test_metabol_v02.py
- test_metabol_v04.py
- test_metabolite_ccc_schema.py
- test_mol.py
- test_mt_detect.py
- test_protein.py
- test_roe.py
- test_sample_metadata_alignment.py
- test_sanger.py
- test_scdblfinder_qc.py
- test_scenic_grn_gene_names.py
- test_set_seed.py
- test_single_batch_cca.py
- test_single_batch_scvi_family.py
- test_single_rpca.py
- test_synbio_biosecurity.py
- test_synbio_community_parts.py
- test_synbio_context.py
- test_synbio_coupling.py
- test_synbio_crispr.py
- test_synbio_dbtl.py
- test_synbio_discrete.py
- test_synbio_dna_layer.py
- test_synbio_exports.py
- test_synbio_gpu.py
- test_synbio_kinetics_asr.py
- test_synbio_manufacturability.py
- test_synbio_number_regressions.py
- test_synbio_perturb.py
- test_synbio_reconstruct.py
- test_synbio_strain_thermo.py
- test_tsne_n_components.py
- test_web_kernel_service.py
- test_web_start_server.py
- .gitignore
- .gitmodules
- default.ipynb
- install.sh
- LICENSE
- make.bat
- Makefile
- MANIFEST.in
- omicverse_guide
- pyproject.toml
- README.md
- requirements-latest.txt
- requirements.txt
- SECURITY.md
- setup.cfg
- setup.py
- WORKFLOW.md
# Installation Guide
1. Get the code
git clone https://github.com/omicverse/omicverse
Downloads the entire project code from GitHub to your computer.
cd omicverse
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install "omicverse[jarvis]"
Installs the package published on PyPI directly β no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Python
EasyPrerequisites
pip install -e "omicverse[mcp]"
Installs the Python libraries listed in requirements.txt (or similar).
python -m omicverse.mcp # or: omicverse-mcp
Runs the Python script (or module).
python -m omicverse.mcp --phase P0 # core pipeline tools only
Runs the Python script (or module).
pip install "omicverse[jarvis]"
Installs the package published on PyPI directly β no need to clone the source.
pip install -e .[tests]
Installs the Python libraries listed in requirements.txt (or similar).
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
4. Make
MediumPrerequisites
- Git Needed to download the project code from GitHub.
- Make Usually pre-installed on Linux/macOS. On Windows, install separately (e.g. via MSYS2 or WSL).
make
Compiles the code based on the generated build configuration to produce an executable.
If it finishes without errors, it worked. Try running the generated executable directly.
// repository documentation
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