# 使用 Homebrew 安装 alevin-fry 查看 alevin-fry 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:alevin-fry ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install alevin-fry ``` 证据: local Homebrew formula metadata ## 软件包事实 - **软件包键:** brew:alevin-fry - **软件包管理器:** Homebrew - **版本:** 0.16.2 - **来源摘要:** Efficient and flexible tool for processing single-cell sequencing data - **主页:** - **仓库:** - **最后更新:** 2026-07-10T07:02:57Z - **已生成:** 2026-08-03T19:37:03+00:00 ## 可执行文件 - alevin-fry (别名) ## 安装行为 - Bottle: 不可用 ## 版本和新鲜度 - 页面生成时间: 2026-08-03 - 管理器版本: 0.16.2 ## 项目历史与用法 alevin-fry is a Rust command-line suite for rapid, accurate, and memory-frugal processing of single-cell and single-nucleus sequencing data. It is a bioinformatics package where packaging matters because users often need reproducible pipelines more than interactive software. ### 项目历史 The official README says alevin-fry consumes RAD files produced by piscem or salmon alevin, generates permit lists, and estimates distinct molecules per gene per cell. The project focuses on safety, accuracy, time efficiency, and memory efficiency. The README and documentation present alevin-fry as the successor to alevin. It subsumes core alevin features, adds capabilities, improves performance, and is where the maintainers expect most future method development to happen, while salmon alevin remains maintained for users not ready to migrate. The project was described in the 2022 Nature Methods paper 'Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data.' Its changelog shows active releases through the 0.9 series, including USA-mode support, UMI resolution modes, dependency updates, and command-line validation improvements. ### 采用历史 The official README documents Bioconda availability for x86 Linux and macOS, crates.io installation through Cargo, and source builds with Cargo. The supplied package facts add Homebrew packaging, while the README points to Bioconda badges, tutorials, GitHub discussions, and downstream R/Bioconductor loading paths. The adoption story is workflow-oriented: alevin-fry is meant to sit in pipelines with piscem or salmon upstream and fishpond, alevinQC, pyroe, or SingleCellExperiment downstream. The project also recommends simpleaf as a wrapper/workflow runner to make common reference-building and quantification workflows easier. ### 使用方式 Users typically produce RAD files with piscem or salmon alevin, then use alevin-fry commands such as permit-list generation, collation, quantification, and inference. The Read the Docs site organizes this around commands including `generate-permit-list`, `collate`, `quant`, `infer`, and `atac`. Installation is intentionally package-manager friendly: `conda install -c bioconda alevin-fry`, `cargo install alevin-fry`, Homebrew packaging, or a direct source build with `cargo build --release`. ### 为什么软件包爱好者会关心 alevin-fry matters to package nerds because it is a scientific CLI whose real unit of use is the reproducible workflow. Versioned binaries, Bioconda, Cargo, Homebrew, and documentation all reduce friction for lab pipelines and HPC environments. It also shows the Rust-in-bioinformatics pattern: performance-sensitive command-line genomics tools distributed through both language-native crates and scientific package channels. ### 时间线 - 2021-06-29: bioRxiv preprint posted for alevin-fry. - 2021-07-22: Changelog records 0.4.1 with metadata/output changes. - 2021-10-16: 0.4.2 added USA mode support to `infer`. - 2022-03-01: Nature Methods paper published. - 2022-06-01: 0.6.0 added UMI resolution and command-line validation work. - 2022-10-11: 0.8.0 fixed force-cells and expect-cells parsing. - 2024-03-08: 0.9.0 released with libradicl compatibility work. ### Related projects - The official README names piscem and salmon as RAD-file producers; simpleaf as a wrapper/workflow runner; pyroe for enhanced transcriptome construction; fishpond for R ingestion; and alevinQC for quality control. - The documentation also connects alevin-fry output to Bioconductor's SingleCellExperiment ecosystem. ### 来源 - - - - - source_facts.package-manager ## 安全说明 没有找到 alevin-fry 的匹配本地密钥处理 manifest。Nucleus 软件包元数据仍在此发布，以便未来覆盖拥有稳定的软件包 URL。 ## Combined YAML source View the package source record on GitHub. [combined/alevin-fry.yml](https://github.com/mxcl/pkgdb/blob/main/combined/alevin-fry.yml) ## 来源 - pkg.so package database - Geiger risk classifier - curated package history - pkgdb category and tag curation - cross-ecosystem install command graph