# CyteArc

> Out-of-core, provenance-backed single-cell analysis for RNA, ATAC, protein, and matched multi-omic data. This documentation is published from the master branch and covers supported workflows, public APIs, and their limitations.

Documentation revision: fccee7b6e0c167e47ce605c8d292fba5b567ebfe. Links below open plain-text documentation.

- [Home](https://docs.nygen.io/CyteArc/index.txt): choose a first example or find a guide for your analysis

## Getting started

- [Quick start](https://docs.nygen.io/CyteArc/quickstart/index.txt): inspect a prepared analysis of 100,000 Tabula Sapiens cells, then run the RNA pipeline
- [Remote dataset mounting](https://docs.nygen.io/CyteArc/tutorials/remote-stores/index.txt): plot the Tabula Sapiens atlas, save a local cell selection, and reopen it while counts stay remote
- [Installation](https://docs.nygen.io/CyteArc/installation/index.txt): supported Python versions and installation paths

## scRNA-seq analysis

- [PBMC analysis](https://docs.nygen.io/CyteArc/tutorials/scrna-seq/index.txt): interpret a prepared PBMC run with marker evidence
- [Quality control](https://docs.nygen.io/CyteArc/tutorials/quality-control/index.txt): modality-aware and sample-aware filtering
- [Highly variable genes](https://docs.nygen.io/CyteArc/tutorials/feature-selection/index.txt): feature-set diagnostics
- [Dimensionality reduction](https://docs.nygen.io/CyteArc/tutorials/dimensionality-reduction/index.txt): PCA dimensions and layout comparison
- [Neighborhood graph](https://docs.nygen.io/CyteArc/tutorials/graph-construction/index.txt): granular normalization, reduction, neighbours, and graphs
- [Clustering](https://docs.nygen.io/CyteArc/tutorials/clustering/index.txt): Leiden, Paris, stability, connectivity, and markers
- [Analysis reuse](https://docs.nygen.io/CyteArc/tutorials/reuse-and-tracing/index.txt): change the neighbour count without rerunning normalization, PCA, or the search index
- [Cell type annotation](https://docs.nygen.io/CyteArc/tutorials/annotation/index.txt): marker interpretation and label assignment
- [Gene-set scoring](https://docs.nygen.io/CyteArc/tutorials/gene-set-scoring/index.txt): AUCell and WAGGR activity scores
- [Cell-cycle scoring](https://docs.nygen.io/CyteArc/tutorials/cell-cycle/index.txt): canonical phase scoring
- [Visualization](https://docs.nygen.io/CyteArc/tutorials/plotting/index.txt): embedding, marker, hierarchy, and trajectory displays
- [Imputation](https://docs.nygen.io/CyteArc/tutorials/imputation/index.txt): graph diffusion for exploratory visualization

## scATAC-seq and multimodal

- [scATAC-seq](https://docs.nygen.io/CyteArc/tutorials/scatac-seq/index.txt): peak filtering, LSI, graph construction, clustering, and gene scores
- [CITE-seq](https://docs.nygen.io/CyteArc/tutorials/cite-seq/index.txt): matched RNA and ADT analysis with WNN integration
- [TEA-seq](https://docs.nygen.io/CyteArc/tutorials/tea-seq/index.txt): prepared RNA, ATAC, and protein analysis with three-way WNN
- [WNN and SNN integration](https://docs.nygen.io/CyteArc/tutorials/multimodal-diagnostics/index.txt): compare SNN and WNN and inspect modality weights
- [HTO demultiplexing](https://docs.nygen.io/CyteArc/tutorials/hto-demultiplexing/index.txt): sample-tag classification and Seurat comparison

## Integration and mapping

- [CyteBase composite datasets](https://docs.nygen.io/CyteArc/tutorials/composite-datasets/index.txt): jointly analyze remote datasets, compare Harmony correction, and reopen saved results while counts stay in their sources
- [Dataset merging](https://docs.nygen.io/CyteArc/tutorials/dataset-merging/index.txt): compatible stores and an uncorrected joint baseline
- [Harmony batch correction](https://docs.nygen.io/CyteArc/tutorials/batch-correction/index.txt): Harmony, batch mixing, and biological conservation
- [Reference mapping and label transfer](https://docs.nygen.io/CyteArc/tutorials/mapping-and-label-transfer/index.txt): fixed-reference projection

## Differential expression

- [Donor-level comparisons](https://docs.nygen.io/CyteArc/tutorials/condition-comparisons/index.txt): matched donor-level testing and its limits
- [Pseudobulk export](https://docs.nygen.io/CyteArc/tutorials/pseudobulk-and-differential-expression/index.txt): biological-replicate aggregation and export

## Trajectory analysis

- [Pseudotime](https://docs.nygen.io/CyteArc/tutorials/pseudotime/index.txt): supervised sources and sinks
- [Expression dynamics](https://docs.nygen.io/CyteArc/tutorials/expression-dynamics/index.txt): feature profiles and modules
- [Fate mapping](https://docs.nygen.io/CyteArc/tutorials/fate-mapping/index.txt): multiple terminal outcomes
- [Trajectory validation](https://docs.nygen.io/CyteArc/tutorials/trajectory-validation/index.txt): boundary, graph, statistical, and numerical checks

## Data management

- [Import and export](https://docs.nygen.io/CyteArc/tutorials/import-and-export/index.txt): source formats, saved Seurat import, and output contracts
- [Scanpy users](https://docs.nygen.io/CyteArc/scanpy/index.txt): workflow mapping and H5AD exchange
- [Seurat users](https://docs.nygen.io/CyteArc/seurat/index.txt): workflow mapping, RDS import, and WNN differences
- [Data model comparison](https://docs.nygen.io/CyteArc/scanpy-and-seurat/index.txt): how objects, selections, and saved results differ between tools
- [Cell and feature metadata](https://docs.nygen.io/CyteArc/tutorials/data-organization/index.txt): assays, cell data, feature data, and metadata
- [Provenance](https://docs.nygen.io/CyteArc/concepts/provenance/index.txt): artifacts, reuse, lineage, and limits
- [Custom analyses](https://docs.nygen.io/CyteArc/tutorials/custom-analyses/index.txt): public extension and export boundaries

## Public datasets

- [CyteBase catalog](https://docs.nygen.io/CyteArc/tutorials/cytebase/index.txt): search cloud-hosted datasets, inspect annotations, and mount a published store
- [COVID-19 atlas case study](https://docs.nygen.io/CyteArc/tutorials/cytebase-covid19/index.txt): compare donors using metadata, the published UMAP, and gene summaries

## Reference

- [Memory and execution](https://docs.nygen.io/CyteArc/concepts/memory-and-execution/index.txt): choose budgets and workers, inspect run reports, and understand memory reservations
- [Remote storage configuration](https://docs.nygen.io/CyteArc/reference/remote-storage/index.txt): object-store credentials, mount behavior, and scratch space for reductions
- [Methods and limitations](https://docs.nygen.io/CyteArc/reference/methods/index.txt): supported workflows, implemented methods, validation evidence, and scope
- [FAQ](https://docs.nygen.io/CyteArc/reference/faq/index.txt): concise method and interoperability answers
- [Glossary](https://docs.nygen.io/CyteArc/reference/glossary/index.txt): CyteArc concepts and terms

## API reference

- [API overview](https://docs.nygen.io/CyteArc/api/index.txt): exact public signatures and result contracts
- [DataStore](https://docs.nygen.io/CyteArc/api/datastore.txt): open stores, select cells and features, run analyses, and access saved results
- [Analysis pipelines](https://docs.nygen.io/CyteArc/api/pipeline.txt): configure RNA pipelines, inspect durable runs, and access frozen outputs
- [Graph construction](https://docs.nygen.io/CyteArc/api/graph_construction.txt): normalization, reduction, neighbour search, and connectivity stages
- [Reference mapping](https://docs.nygen.io/CyteArc/api/mapping.txt): build references, project query cells, and transfer labels
- [Integration and metrics](https://docs.nygen.io/CyteArc/api/integration.txt): WNN, SNN, Harmony, and integration diagnostics
- [Assays and metadata](https://docs.nygen.io/CyteArc/api/assays.txt): assay types, count blocks, cell and feature metadata, and selections
- [Artifacts and lineage](https://docs.nygen.io/CyteArc/api/artifacts.txt): find saved results, trace their inputs, and summarize analyses
- [Import and export](https://docs.nygen.io/CyteArc/api/import_export.txt): readers, writers, dataset merging, and storage controls
- [Plotting](https://docs.nygen.io/CyteArc/api/plotting.txt): embeddings, expression, clusters, trajectories, and diagnostics
- [Utilities](https://docs.nygen.io/CyteArc/api/utilities.txt): store loading, computation settings, gene sets, logging, and progress
- [CyteBase API](https://docs.nygen.io/CyteArc/api/cytebase.txt): catalog queries, metadata-only DatasetEntry objects, remote DataStore access, imported embedding helpers, and writable mounts with remote counts

## Developers

- [Contributing](https://docs.nygen.io/CyteArc/developers/contributing/index.txt): local workflow and required checks
- [Architecture](https://docs.nygen.io/CyteArc/developers/architecture/index.txt): package boundaries and code placement
- [Zarr internals](https://docs.nygen.io/CyteArc/developers/zarr-internals/index.txt): on-disk layout for maintainers
- [Operation revisions](https://docs.nygen.io/CyteArc/developers/operation-revisions/index.txt): maintainer rules for invalidating saved computations after algorithm changes