Cytome focuses on managing and streaming multi-omics single-cell biology data in a portable single-file format. It is catalogued under Databases (SQL, NoSQL, vector, graph) on PulseGate.

Who should use cytome?

cytome is an open-source project built for bioinformatics researchers and computational biologists.

Does cytome have a free plan?

Yes — cytome is open source under the BSD-3-Clause license and free to use.

What platforms does cytome run on?

cytome runs on the command line. It can also be self-hosted.

Is cytome still active?

The GitHub repository shows 3 commits in the last 90 days.

What are alternatives to cytome?

Similar projects tracked by PulseGate include SQLified, RawTree, and meta-agents-db.

cytome is developed by GeneCell.

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cytome

Name: cytome
Author: GeneCell

PyPIInfrastructure

cytome is an open-source single-file multi-omics data format for single-cell biology. It supports single-cell genomics workflows, including scRNA-seq and scATAC-seq data, with SQLite storage and streaming access.

Open SourceBSD-3-ClauseCLISelf-hosted

Visit PyPI

Overview

5 features

In the Databases (SQL, NoSQL, vector, graph) space, cytome takes a focused approach. It focuses on managing and streaming multi-omics single-cell biology data in a portable single-file format. cytome is an open-source project aimed at bioinformatics researchers and computational biologists. cytome is open source under the BSD-3-Clause license. It ships for the command line, and it can be self-hosted.

GeneCell builds and maintains cytome, and it first shipped in 2026. The project is developed in the open on GitHub with 3 commits in the last 90 days. Among its 5 catalogued features are single-file format, multi-omics data, and SQLite storage.

Summary written by a language model from the project’s public pages.

Single-file format
Multi-omics data
SQLite storage
Streaming access
Single-cell support

Built with & integrations

Connectors

github

Runs on

CLISelf-hosted

Trust & compliance

License

BSD-3-Clause

Verified signals

HTTPSOpen Source GitHubActive maintenance

Indexing history

What PulseGate has recorded for this listing

Indexed10 Aug · 18:48 UTC
cytome verified against its public source
Source: PulseGate · Open

Frequently asked questions about cytome

What is cytome?: Cytome focuses on managing and streaming multi-omics single-cell biology data in a portable single-file format. It is catalogued under Databases (SQL, NoSQL, vector, graph) on PulseGate.
Who should use cytome?: cytome is an open-source project built for bioinformatics researchers and computational biologists.
Does cytome have a free plan?: Yes — cytome is open source under the BSD-3-Clause license and free to use.
What platforms does cytome run on?: cytome runs on the command line. It can also be self-hosted.
Is cytome still active?: The GitHub repository shows 3 commits in the last 90 days.
What are alternatives to cytome?: Similar projects tracked by PulseGate include SQLified, RawTree, and meta-agents-db.SQLified RawTree meta-agents-db
Who makes cytome?: cytome is developed by GeneCell.
How long has cytome been around?: cytome first shipped in 2026.

At a glance

Platforms: Cli
Languages: English
Open source: Yes (GitHub)
License: BSD-3-Clause
First seen: 10 Aug 2026
Built for: bioinformatics researchers and computational biologists
Model: Open source
Solves: Managing and streaming multi-omics single-cell biology data in a portable single-file format.

Registered as

GitHub: genecell/cytome
PyPI: cytome

Developer

GeneCell

Solo developer

GitHub

Open source

View on GitHub

Stars: 0
Forks: 0
Open issues: 0
Last commit: 10 Aug 2026
Commits 90d: 3
Contributors: 1
Authorship: Solo
Default branch: master

Index record

Identity confidence: Low · 64
Indexed: 10 Aug 2026
Lifecycle: Alive
First seen: Aug 2026
Last seen: 10 Aug 2026

Identity audit (13)

Slug: cytome-pypi-org
Lifecycle state recorded: 10 Aug 2026
Verification state: Indexed for public listing
Listing state: Listed: yes
Index status: Included in index
Latest evidence snapshot: 10 Aug 2026
Timeline basis: Indexed-at chronology (no inferred launch/funding milestones).
Name from: Written by a language model from the project's public pages.
Category from: Assigned by a language model.
Summary from: Written by a language model from public pages.
Languages from: Detected by a language model from page content.
Last updated: 10 Aug 2026
Canonical URL: https://pypi.org/project/cytome

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