macOS
Homebrewverifiziert · 100%
brew install oarfishlocal Homebrew formula metadata
brew
oarfish mit Homebrew installieren
Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für oarfish in AI-Agent-Workflows.
Installation
Weitere Installationsbefehle
Überblick
Paketzusammenfassung
Long read RNA-seq quantification
Projektlinks
Befehle und Aliase
- oarfish
Verlauf
Projektgeschichte und Nutzung
oarfish is a Rust tool from COMBINE-lab for transcript-level quantification from long-read RNA-seq data, including Oxford Nanopore cDNA/direct RNA and PacBio reads. It allocates multi-mapping reads probabilistically with an expectation-maximization model and adds coverage information to improve isoform-level estimates.
Projektgeschichte
The GitHub repository was created on June 27, 2022. The project emerged from the COMBINE-lab lineage of RNA-seq quantification tools, applying probabilistic transcript-assignment ideas to long-read sequencing rather than short-read workflows.
Adoptionsgeschichte
The method was described in the 2024 preprint and later Bioinformatics paper "Enhanced probabilistic modeling leads to improved accuracy in long-read transcriptome quantification." Distribution through GitHub releases, Cargo, Bioconda, and Homebrew made it available to both Rust users and bioinformatics workflow environments.
Wie es verwendet wird
oarfish accepts transcriptome BAM alignments, raw reads that it maps internally, genome reads that are spliced-aligned and projected to transcripts, or existing genome BAMs projected against a transcript annotation. The common workflow is to supply long-read RNA-seq data plus transcript sequences or annotation, then produce transcript abundance estimates with optional bootstrap uncertainty and coverage modeling.
Warum Paket-Nerds sich dafür interessieren
For package watchers, oarfish is a good example of scientific software moving through several distribution channels at once: a Rust codebase and Cargo package, prebuilt GitHub release binaries, Bioconda recipes for workflow managers, and a Homebrew formula for local command-line installs.
Zeitleiste
- 2022-06-27: COMBINE-lab/oarfish repository was created.
- 2024-02-28: The oarfish preprint was posted to bioRxiv.
- 2026-06-07: GitHub release v0.10.0 was published.
Related projects
- The documentation compares or connects oarfish with NanoCount-style filters, minimap2 and other aligners for BAM input, rammap for in-process long-read mapping, and bramble for genome-to-transcript projection.
Quellen
- https://academic.oup.com/bioinformatics/article/41/Supplement_1/i304/8199410
- https://api.github.com/repos/COMBINE-lab/oarfish
- https://bioconda.github.io/recipes/oarfish/README.html
- https://formulae.brew.sh/formula/oarfish
- https://github.com/COMBINE-lab/oarfish
- https://github.com/COMBINE-lab/oarfish/releases
- https://pubmed.ncbi.nlm.nih.gov/38464200/
- https://www.biorxiv.org/content/10.1101/2024.02.28.582591v1
Sicherheitslage
Risikostufe: grün
narrow executable package without higher-risk signals.
Risikoklassifikator
grün Risiko · niedrig Konfidenz · appliance
Warum
- narrow executable package without higher-risk signals
Signale
- metadata:no-higher-risk-signals
Installationsverhalten
- In den Formelmetadaten ist kein Homebrew-Post-install-Hook erfasst.
- Homebrew-Bottle-Metadaten sind für 6 Plattformziele verfügbar.
- Build-Metadaten listen 1 Build-Abhängigkeiten.
Empfohlene Prüfung
Prüfe vor unbeaufsichtigter Agent-Nutzung, ob das Tool Klartext-Credentials liest, Remote-Zustand schreibt, Artefakte veröffentlicht oder Plugins ausführt.
Executables
Installierte Executables
| Befehl | Art | Sichtbarkeit | Hinweis |
|---|---|---|---|
oarfish | cli | globales Executable |
Aktualität
Version und Aktualität
Diese Signale trennen das Alter der Seitengenerierung, Aktivität des Paketmanagers und Upstream-Release-Vergleich. Versionsrückstand wird nur gemeldet, wenn eine Evidenz-URL und vergleichbare Versionen vorhanden sind.
Seite generiert2026-07-08
Manager-Version0.10.0
Manager aktualisiert2026-06-21
lokale DatenOK
Upstreamaktuell
neueste erkannte Versionv0.10.0
https://github.com/COMBINE-lab/oarfish
- OKEs wurden keine Aktualitätswarnungen generiert.
Installationsmetadaten
Paketmetadaten
| Paketschlüssel | brew:oarfish |
|---|---|
| Version | 0.10.0 |
| Paketmanager | Homebrew |
| Paketmanager-Seite | https://formulae.brew.sh/formula/oarfish |
| Homepage | https://github.com/COMBINE-lab/oarfish |
| Repository | https://github.com/COMBINE-lab/oarfish |
| Upstream-Dokumentation | https://github.com/COMBINE-lab/oarfish#readme |
| Lizenz | BSD-3-Clause |
| Quellarchiv | https://github.com/COMBINE-lab/oarfish/archive/refs/tags/v0.10.0.tar.gz |
| Zuletzt aktualisiert | 2026-06-21T00:20:16Z |
| Pulse | updated |
| Build-Abhängigkeiten | rust |
| Von macOS bereitgestellte Bibliotheken | bzip2 |
| Bottle | verfügbar (auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | nicht definiert |
| Dienst | keiner deklariert |
Registry-Fakten
Details aus der Quelldatenbank
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | oarfish |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
Quellspur
Aus Repository-Daten generiert
Diese Seite wird von av-web aus dem privaten Paket-SQLite-Artefakt bereitgestellt, das scripts/generate-pkg-sqlite.py erstellt.
Combined YAML source
View the package source record on GitHub.
Verwendete Quellen
- Geiger risk classifier
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- package relationship graph
- package version freshness
- package-page enrichment