add-bot
Add seabbs-bot as a collaborator with push permissions to a repository
analyzing-research-papers
Expert methodology for analyzing and summarizing research papers, extracting key contributions, methodological details, and contextualizing findings. Use when reading papers from PDFs, DOIs, or URLs to create structured summaries for researchers.
commit
Create a well-structured commit with conventional format and proper git identity
create-note
Import a markdown file into Obsidian library and format it as a note
docs
Check that all code has appropriate documentation and fix gaps
format-note
Format an Obsidian note with tags and link it from today's daily note
github-dashboard
GitHub dashboard update with notifications, PR status, issue triage, and action items
grant-application-setup
Expert guidance for setting up and organising research grant applications following established patterns for UKRI, EU, and other funding bodies
grant-compliance-checking
Expert knowledge of research grant compliance requirements, deliverables tracking, and funder expectations. Use when reviewing work against grant specifications, preparing progress reports, or ensuring alignment with funding requirements from NSF, NIH, EU, and other agencies.
improve-coverage
Improve test coverage by identifying gaps and generating meaningful tests
issue-reply
Post a helpful reply to a GitHub issue
issue-summary
Summarise a GitHub issue conversation with focus on the last message
lint
Lint, format, and optionally commit changes
literature-search
Search local bibliography files and Paperpile for relevant papers
minutes
Create structured meeting minutes from a transcript
paper-summary
Summarise an academic paper from URL, DOI, or file path
pr
Create a pull request based on a GitHub issue with analysis, implementation, QA, and PR creation
preprint-search
Search for new preprints in infectious disease modelling from arXiv, medRxiv, and bioRxiv
project-organization
Expert guidance for setting up and organizing research software projects following Sam Abbott's established patterns for R packages, Julia packages, and research projects
r-development
Expert guidance for R package development following best practices for devtools, testthat, roxygen2, and R ecosystem tools
repo-activity
Analyse GitHub repository activity including issues, PRs, contributors, and engagement
repo-summary
Analyse a GitHub repository combining activity metrics with code development insights
review
Perform a code review with linting, standards checking, and priority-ranked findings
scan-issues
Scan repositories and identify issues that Claude Code can efficiently handle
stan-development
Expert guidance for Stan probabilistic programming language development, including modern syntax, cmdstanr/cmdstanpy integration, and testing patterns
taskfile-automation
Expert guidance for using Task (taskfile.dev) automation tool to discover and execute project development commands
test
Run tests iteratively fixing code or tests until all pass, then commit
uk-news
Create a UK news summary from BBC and Guardian sources
update-deps
Review and update project dependencies safely with incremental testing
academic-writing-standards
Expert knowledge of academic writing standards for peer-reviewed papers, including citation integrity, style compliance, clarity, and scientific writing best practices. Use when reviewing or editing academic manuscripts, papers, or research documentation.
julia-development
Expert guidance for Julia package development following SciML standards, Distributions.jl patterns, and Julia ecosystem best practices