# ASAP

> ASAP (Automated Single-cell Analysis Pipeline) is a collaborative web platform for analyzing and visualizing single-cell RNA-seq and related omics data. Developed at EPFL and listed among SIB resources.

ASAP guides users through a modular analysis pipeline on large single-cell datasets: import and parsing, filtering, normalization, clustering, differential expression, doublet calling, and interactive UMAP/t-SNE visualization. Public projects and JSON exports are available via the REST API.

## Getting started

- [Welcome](https://asap.epfl.ch/): Platform home and project browser
- [Guided tours](https://asap.epfl.ch/guided-tours): Interactive walkthroughs of the application
- [FAQ](https://asap.epfl.ch/home/faq): Frequently asked questions

## Documentation

- [File formats](https://asap.epfl.ch/home/file_format): Supported upload and export formats
- [API documentation](https://asap.epfl.ch/api-doc): Interactive OpenAPI reference for JSON endpoints
- [OpenAPI spec](https://asap.epfl.ch/api/openapi.yaml): Machine-readable API specification
- [News](https://asap.epfl.ch/news_items): Platform announcements and updates
- [Releases](https://asap.epfl.ch/versions): ASAP version history and release notes
- [Project types](https://asap.epfl.ch/project_types): Available pipeline types and configurations
- [Cell metadata schema](https://asap.epfl.ch/ontology_term_types): Cell metadata fields used for annotations
- [Cross-references](https://asap.epfl.ch/home/cross_references): External identifier types (GEO, ArrayExpress, BioProject, SRA)

## Data and atlases

- [Public projects](https://asap.epfl.ch/projects): Browse and clone shared analysis projects
- [Atlases](https://asap.epfl.ch/atlases): Fly Cell Atlas and Human Cell Atlas entry points
- [scFAIR compliance](https://asap.epfl.ch/compliance): Validate projects and files against scFAIR schema rules
- [File compliance check](https://asap.epfl.ch/compliance/file-check): Standalone H5AD/Loom compliance check

## Citation

- [Citing ASAP](https://asap.epfl.ch/home/citing): Primary publications (Bioinformatics 2017; NAR 2020) and DOIs

## Optional

- [Contact](https://asap.epfl.ch/home/contact): Reach the ASAP team
- [Sitemap](https://asap.epfl.ch/sitemap.xml): Full list of public URLs
- [GitHub discussions](https://github.com/DeplanckeLab/ASAP/discussions): Community Q&A
- [GitHub issues](https://github.com/DeplanckeLab/asap_web/issues): Bug reports and feature requests