# oarfish を Homebrew でインストール oarfish のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。 ## インストール ```sh sudo av install brew:oarfish ``` 追加のインストールコマンド: ### macOS - Homebrew (100%): ```sh brew install oarfish ``` 証拠: local Homebrew formula metadata ## パッケージ情報 - **パッケージキー:** brew:oarfish - **パッケージマネージャ:** Homebrew - **パッケージマネージャページ:** - **バージョン:** 0.10.0 - **ソース概要:** Long read RNA-seq quantification - **ホームページ:** - **リポジトリ:** - **上流ドキュメント:** - **ライセンス:** BSD-3-Clause - **ソースアーカイブ:** - **最終更新:** 2026-06-21T00:20:16Z - **生成日時:** 2026-07-08T18:08:21+00:00 ## 実行可能ファイル - oarfish (cli) - oarfish (エイリアス) ## ビルド依存関係 - rust ## macOS 提供ライブラリ - bzip2 ## インストール挙動 - post-install フック: 未定義 - Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## バージョンと鮮度 - ページ生成日: 2026-07-08 - マネージャ版: 0.10.0 - マネージャ更新日: 2026-06-21 - ローカルデータ: OK - 上流リポジトリ: https://github.com/COMBINE-lab/oarfish - 検出された最新: v0.10.0 (最新) ## プロジェクトの歴史と使われ方 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. ### プロジェクトの歴史 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. ### 採用の歴史 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. ### 使われ方 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. ### パッケージ好きにとっての重要性 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. ### タイムライン - 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. ### ソース - - - - - - - - ## セキュリティノート narrow executable package without higher-risk signals. - **Geiger リスク:** グリーン / 低 - narrow executable package without higher-risk signals ## ソースデータベース詳細 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** oarfish - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## 関連リンク - [Source-control packages](https://www.automicvault.com/ja/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Language runtime packages](https://www.automicvault.com/ja/pkg/language-runtime-packages/) - Matched language runtime, compiler, or interpreter metadata. - [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [rust](https://www.automicvault.com/ja/pkg/brew/rust/) - Build dependency declared by Homebrew. - [flye](https://www.automicvault.com/ja/pkg/brew/flye/) - Shares av.db curated category or tags: bioinformatics, cli, long-read-sequencing, science. - [kallisto](https://www.automicvault.com/ja/pkg/brew/kallisto/) - Shares av.db curated category or tags: bioinformatics, cli, rna-seq, science. - [rna-star](https://www.automicvault.com/ja/pkg/brew/rna-star/) - Shares av.db curated category or tags: bioinformatics, cli, rna-seq, science. - [stringtie](https://www.automicvault.com/ja/pkg/brew/stringtie/) - Shares av.db curated category or tags: bioinformatics, cli, rna-seq, science. - [abpoa](https://www.automicvault.com/ja/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/ja/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abyss](https://www.automicvault.com/ja/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [adapterremoval](https://www.automicvault.com/ja/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science. ## Combined YAML source View the package source record on GitHub. [combined/oarfish.yml](https://github.com/automic-vault/db/blob/main/combined/oarfish.yml) ## ソース - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - cross-ecosystem install command graph