Build installable BSgenome R packages from NCBI or Ensembl assemblies.
npx skills add https://github.com/JohnnyChen1113/autoBSgenome --skill autobsgenome
Please help me install this Agent Skill. Skill: autobsgenome Source: https://github.com/JohnnyChen1113/autoBSgenome/tree/main Command: npx skills add https://github.com/JohnnyChen1113/autoBSgenome --skill autobsgenome
It solves the problem of not having a required BSgenome reference package for your organism, which blocks Bioconductor tools that depend on standardized genome access (and forces users into a difficult, error-prone manual build process).
Use the autobsgenome skill to build an organism package for your missing BSgenome dependency by triggering the API with your NCBI GCF_/GCA_ accession and then installing the returned tar.gz URL in R.
High-intent search queries and answers about installing and using this skill.
Building a BSgenome package requires fetching a specific genome assembly from NCBI or Ensembl, preparing the sequences, and generating seed metadata. This Skill automates that entire process, returning a downloadable tar.gz artifact ready for install.packages in R.
Yes, you can automate BSgenome package generation through API-driven build triggering and status polling. This provides a standardized BSgenome backend required by downstream Bioconductor tools like TSSr, motifmatchr, and ChIPseeker for repeatable automated workflows.
Handling circular sequences for mitochondria, chloroplasts, or plasmids requires specific metadata generation during the BSgenome build process. This Skill automatically detects and applies circular-sequence-aware metadata when preparing the genome assembly package.
Yes, autobsgenome works by accepting either an NCBI GCF_ or GCA_ accession number, or an Ensembl species URL. It fetches the target genome assembly directly from these databases to construct the installable R package artifact.
Bioconductor analyses fail because downstream tools depend on standardized genome access provided by a BSgenome reference package. When the package is missing, the dependency is unmet; autobsgenome solves this by building the required package on demand.
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