Reporting Adverse Events
maziyarpanahi/openmed
Structures adverse-event mentions that OpenMed extracts into FAERS / ICH E2B(R3) reportable fields — suspect drug, reaction (MedDRA PT), seriousness criteria, and outcome.
The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products.
Custom licenceAuto-check passed
Install Bioconductor Faers
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-faers --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/general/faers .claude/skills/bioconductor-faers && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "bioconductor-faers" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/faers into .claude/skills/bioconductor-faers/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-faers", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/faersType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-faers --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/general/faers .agents/skills/bioconductor-faers && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bioconductor-faers" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/faers into .agents/skills/bioconductor-faers/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-faers", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-faers --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/general/faers .cursor/skills/bioconductor-faers && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bioconductor-faers" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/faers into .cursor/skills/bioconductor-faers/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-faers", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/bioMate-AI/biomate-bioconductor-kb.git --path skills/general/faers--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-faers --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/general/faers .gemini/skills/bioconductor-faers && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bioconductor-faers" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/faers into .gemini/skills/bioconductor-faers/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-faers", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-faersInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/general/faers .github/skills/bioconductor-faers && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bioconductor-faers" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/faers into .github/skills/bioconductor-faers/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-faers", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-faers --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/general/faers .opencode/skills/bioconductor-faers && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bioconductor-faers" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/faers into .opencode/skills/bioconductor-faers/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-faers", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
bioconductor-faers- GitHub stars
- 804
- Token cost
- ~822 tokens
- SKILL.md length
- 247 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products.
- SKILL.md covers Workflows, When to Use, When NOT to Use and Data Requirements, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Bioconductor Faers is an agent skill from bioMate-AI/biomate-bioconductor-kb. The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.
Its SKILL.md is about 820 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
The repository describes itself as: BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes.
Example prompts
- “/bioconductor-faers”
What it can do on your machine
Read from SKILL.md and the folder at commit c9bd4d8. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are r).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
bioconductor.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Bioconductor Faers loads about 822 tokens when it runs. Until then it costs about 97 tokens; SKILL.md has 247 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 247 words (~822 tokens).
“Input/Output Note: Inputs are year, quarter, and directory paths for FAERS raw data; outputs are standardized FAERS data tables and MedDRA hierarchy mappings.”
- name
- bioconductor-faers
- when_to_use
- Use when: The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and me; FAERS-Pharmacovigilance…
- user-invocable
- false
Files
Just SKILL.md in skills/general/faers of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Faers next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bioconductor Faers this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~822 | Automated safety check: Pass | Custom licence | |
| Reporting Adverse Eventsmaziyarpanahi/openmed | 5.5k | — | ~2.2k | Automated safety check: Pass | Apache-2.0 | |
| Reportmicrosoft/data-formulator | 18k | — | ~1.5k | Automated safety check: Pass | MIT | |
| Adverse Event Narrativeaipoch/medical-research-skills | 1.9k | — | ~3k | Automated safety check: Pass | MIT | |
| Reportalirezarezvani/claude-skills | 28k | 1 repos | ~727 | Automated safety check: Pass | MIT | |
| Bugcrowd Reportingsickn33/agentic-awesome-skills | 47k | 1 repos | ~5.9k | Automated safety check: Pass | MIT |
Similar skills
- Official
Report
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Turn an exploration (threads, findings, charts) into a single Markdown report — note, blog post, executive summary, KPI dashboard, slide brief, or multi-section analytical report, with embedded…
Adverse Event Narrative
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Generates CIOMS I-compliant ICSR narratives from adverse event case data for FDA and EMA regulatory submission.
Report
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Generate test report. An agent skill from alirezarezvani/claude-skills.
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Bugcrowd-specific reporting tactics complementing report-writing
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When the user wants to plan, run, sponsor, speak at, or get pipeline from events — webinars, conferences, trade shows, meetups, dinners, workshops, virtual summits, or user conferences.
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Questions about Bioconductor Faers
What does Bioconductor Faers do?
The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. Bioconductor Faers is an agent skill from bioMate-AI/biomate-bioconductor-kb. The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products.
How do I install Bioconductor Faers in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a claude-code`. Or copy the skill folder (skills/general/faers in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-faers in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Faers in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a codex`. Or copy the skill folder (skills/general/faers in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-faers in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Faers in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-faers -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bioconductor-faers, .gemini/skills/bioconductor-faers, .github/skills/bioconductor-faers and .opencode/skills/bioconductor-faers in your project.
What does Bioconductor Faers need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Faers is instructions for the agent only.
Does Bioconductor Faers access the network?
SKILL.md names 1 domain. As links in the text: bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Faers safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Bioconductor Faers use?
Bioconductor Faers has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Bioconductor Faers use?
About 822 tokens (SKILL.md is roughly 3.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Bioconductor Faers?
Skills that share tags, products or a category with Bioconductor Faers: Reporting Adverse Events (maziyarpanahi/openmed, 5.5k stars), Report (microsoft/data-formulator, 18k stars), Adverse Event Narrative (aipoch/medical-research-skills, 1.9k stars) and Report (alirezarezvani/claude-skills, 28k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Faers?
bioMate-AI (a GitHub organization) maintains it in bioMate-AI/biomate-bioconductor-kb, which has 804 GitHub stars. The repository holds 112 skills in this directory. The repository was last updated on June 20, 2026.
Source: bioMate-AI/biomate-bioconductor-kb on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.