Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
A skill your agent uses when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart.
Install Gokegg Analysis
$ npx skills add aipoch/medical-research-skills --skill gokegg-analysis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills gokegg-analysis --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/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'awesome-med-research-skills/Data Analysis/gokegg' .claude/skills/gokegg-analysis && 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 "gokegg-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gokegg into .claude/skills/gokegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gokegg-analysis", 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/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gokeggType 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 aipoch/medical-research-skills --skill gokegg-analysis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills gokegg-analysis --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'awesome-med-research-skills/Data Analysis/gokegg' .agents/skills/gokegg-analysis && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "gokegg-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gokegg into .agents/skills/gokegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gokegg-analysis", 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 aipoch/medical-research-skills --skill gokegg-analysis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills gokegg-analysis --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'awesome-med-research-skills/Data Analysis/gokegg' .cursor/skills/gokegg-analysis && 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 "gokegg-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gokegg into .cursor/skills/gokegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gokegg-analysis", 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/aipoch/medical-research-skills.git --path 'awesome-med-research-skills/Data Analysis/gokegg'--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 aipoch/medical-research-skills --skill gokegg-analysis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills gokegg-analysis --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'awesome-med-research-skills/Data Analysis/gokegg' .gemini/skills/gokegg-analysis && 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 "gokegg-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gokegg into .gemini/skills/gokegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gokegg-analysis", 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 aipoch/medical-research-skills gokegg-analysisInstalls 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 aipoch/medical-research-skills --skill gokegg-analysis -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'awesome-med-research-skills/Data Analysis/gokegg' .github/skills/gokegg-analysis && 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 "gokegg-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gokegg into .github/skills/gokegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gokegg-analysis", 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 aipoch/medical-research-skills --skill gokegg-analysis -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aipoch/medical-research-skills gokegg-analysis --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'awesome-med-research-skills/Data Analysis/gokegg' .opencode/skills/gokegg-analysis && 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 "gokegg-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gokegg into .opencode/skills/gokegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gokegg-analysis", 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
gokegg-analysis- GitHub stars
- 1.9k
- Token cost
- ~2.7k tokens
- SKILL.md length
- 1,107 words
- Files
- 12 (incl. scripts, references, assets)
- Skills in repo
- 578
- Repo updated
- First seen
- Licence
- MIT
At a glance
A skill your agent uses when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart.
- Performing GO and KEGG enrichment on a gene list from bulk RNA-seq
- SKILL.md covers When To Read External Files, When To Use, Usage and Agent Output, plus 5 more sections
- Runs R scripts from its folder; calls go
- Microarray studies
What it does
Gokegg Analysis is an agent skill from aipoch/medical-research-skills. Use when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart. NOT for single-cell RNA-seq, methylation data, or non-expression data.
Its SKILL.md is about 2.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 16 other files, including scripts, reference files and assets (for example `eval_report_gokegg_result.json`, `references/algorithm.md` and `references/cli-guide.md`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.
When your agent uses it
- Performing GO and KEGG enrichment on a gene list from bulk RNA-seq
- Microarray studies
- Then generating a combined GO/KEGG dot chart
Example prompts
- “/gokegg-analysis”
What it can do on your machine
Read from SKILL.md and the folder at commit 686e09d. 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
Ships 5 files in scripts/ (R), which the agent can run.
Shell commands in SKILL.md call:
go
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Gokegg Analysis loads about 2.7k tokens when it runs, and up to ~6.5k if it reads all its reference files. Until then it costs about 58 tokens; SKILL.md has 1,107 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); the scripts in this folder are not scanned.
SKILL.md
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 1,107 words, ~2,691 tokens.
Download SKILL.mdSave it as
.claude/skills/gokegg-analysis/SKILL.md (or your agent's skills folder). This skill also uses 11 other files; get the full folder from GitHub.- name
- gokegg-analysis
- description
- Use when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart. NOT for single-cell RNA-seq, methylation data, or non-expression data.
- license
- MIT
- author
- AIPOCH
When To Read External Files
| Situation | File To Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md | Statistical methods and formulas |
| Need to run the analysis | scripts/main.R | Full execution command |
| Encounter an error | references/troubleshooting.md | Troubleshooting guidance |
| Need CLI examples | references/cli-guide.md | Parameter usage examples |
When To Use
Use this skill for:
- GO and KEGG enrichment from a gene list derived from bulk RNA-seq or microarray studies
- Supported gene ID types:
SYMBOL,ENSEMBL,ENTREZID - Supported species databases:
org.Hs.eg.db,org.Mm.eg.db,org.Rn.eg.db
Do not use this skill for:
- Single-cell RNA-seq analysis
- Methylation, proteomics, or non-expression omics workflows
- Differential expression testing from raw count matrices
Usage
Main analysis and plotting:
Rscript scripts/main.R --feature "TP53,EGFR,BRCA1,MYC" --output_dir ./output --sp org.Hs.eg.db --gene_type SYMBOL --pvalue_cutoff 0.05 --qvalue_cutoff 0.2 --pAdjustMethod BH --seed 66 --go_top_n 3 --kegg_top_n 3 --format pdf
Notes:
scripts/main.Ris the only command-line entry pointscripts/dochart.Rcurrently provides plotting functions and is sourced byscripts/main.R- If
--go_input,--kegg_input, or--outdirare omitted,main.Rusesoutput_dir/temp/GO_list.rda,output_dir/temp/KEGG_list.rda, andoutput_dir/plotautomatically
Agent Output
On success, the agent should report:
- Whether GO enrichment completed successfully
- Whether KEGG enrichment completed successfully
- The normalized input gene count after trimming and parsing
- The main output directory
- The generated files, especially
GO_df.csv,KEGG_df.csv,GO_list.rda,KEGG_list.rda, and the combined dot chart - The path to
session_info.txt
Post-run checklist:
- Re-parse the original
--featurestring using the documented separator rules and report the deduplicated gene count after trimming - Check
temp/GO_df.csvandtemp/GO_list.rdabefore claiming GO success - Check
temp/KEGG_df.csvandtemp/KEGG_list.rdabefore claiming KEGG success - Check
plot/gokegg_dot_chart.<format>,plot/gokegg_dot_chart_data.csv,plot/gokegg_dot_chart_data.rda, andsession_info.txtbefore claiming full success - Summarize the final result with: parsed gene count, GO status, KEGG status, plot status, output directory, and key output files
On failure, the agent should report:
- The exact
SKILL_*error code - The failing step, such as gene parsing, ID conversion, enrichment, or plotting
- The actionable next step, such as fixing input IDs, checking missing packages, or regenerating
.rdafiles
Parameter Reference
scripts/main.R
| Short | Long | Type | Default | Required | Description |
|---|---|---|---|---|---|
-f | --feature | character | "" | Yes | Gene list separated by commas, Chinese commas, semicolons, tabs, or newlines |
-o | --output_dir | character | ./output/ | No | Main output directory |
-s | --sp | character | org.Hs.eg.db | No | Species database |
-g | --gene_type | character | SYMBOL | No | Input gene ID type |
-p | --pvalue_cutoff | numeric | 0.05 | No | Enrichment p-value cutoff |
-q | --qvalue_cutoff | numeric | 0.2 | No | Enrichment q-value cutoff |
-m | --pAdjustMethod | character | BH | No | P-value adjustment method |
--seed | integer | 66 | No | Random seed | |
--go_input | character | NULL | No | Optional GO .rda; defaults to output_dir/temp/GO_list.rda | |
--kegg_input | character | NULL | No | Optional KEGG .rda; defaults to output_dir/temp/KEGG_list.rda | |
--outdir | character | NULL | No | Plot output directory; defaults to output_dir/plot | |
--go_top_n | numeric | 3 | No | Top GO terms per ontology | |
--kegg_top_n | numeric | 3 | No | Top KEGG pathways | |
-w | --width | numeric | 20 | No | Plot width in cm |
--height | numeric | 16 | No | Plot height in cm | |
--format | character | pdf | No | Plot format: pdf, png, svg | |
--dpi | numeric | 300 | No | DPI for raster output | |
-c | --colors | character | #E41A1C,#FFFF33,#2E86AB,#4DAF4A | No | Colors for GO:BP,GO:CC,GO:MF,KEGG |
--title | character | GO + KEGG Dot Chart | No | Plot title | |
--xlab | character | NULL | No | Horizontal axis label override | |
--ylab | character | NULL | No | Vertical axis label override | |
--dot_size | numeric | 4.5 | No | Dot size | |
--shape | numeric | 19 | No | Dot shape | |
--rotate / --no-rotate | logical flag | TRUE | No | Rotate plot orientation on or off | |
--sorting | character | descending | No | Dot sorting order | |
--label_width | numeric | 35 | No | Label wrap width | |
--title_size | numeric | 12 | No | Title font size | |
--axis_title_size | numeric | 9 | No | Axis title font size | |
--axis_text_size | numeric | 8 | No | Axis text font size | |
--legend_title_size | numeric | 8 | No | Legend title font size | |
--legend_text_size | numeric | 7 | No | Legend text font size | |
--legend_position | character | top | No | Legend position | |
--plot_margin | character | 10,10,10,10 | No | Plot margins: top,right,bottom,left | |
--axis_line_size | numeric | 0.5 | No | Axis line width | |
--axis_ticks_size | numeric | 0.5 | No | Axis tick width | |
--show_grid | logical | FALSE | No | Show grid lines | |
-v | --verbose | logical | FALSE | No | Enable verbose logging |
Input Format
Show full SKILL.md (482 more words)Show less
Main Analysis Input
--featureshould be provided as a gene list- Preferred separator: comma
- Also accepted: Chinese commas, semicolons, tabs, and newlines
- Leading and trailing spaces around each gene are removed automatically with trimming
- The gene ID type must match
--gene_type --spsupports onlyorg.Hs.eg.db,org.Mm.eg.db, andorg.Rn.eg.db
Examples:
TP53,EGFR,BRCA1,MYC
TP53, EGFR, BRCA1, MYC
TP53；EGFR；BRCA1；MYC
TP53\nEGFR\nBRCA1\nMYC
Example command with minimal input:
Rscript scripts/main.R --feature "TP53,EGFR,BRCA1,MYC" --output_dir ./example_output --sp org.Hs.eg.db --gene_type SYMBOL
Example command with custom plotting parameters:
Rscript scripts/main.R --feature "TP53,EGFR,BRCA1,MYC" --output_dir ./example_plot_output --sp org.Hs.eg.db --gene_type SYMBOL --go_top_n 5 --kegg_top_n 8 --colors "#E41A1C,#FFFF33,#2E86AB,#4DAF4A" --title "Custom GO + KEGG Dot Chart" --xlab="-log10(adjusted p-value)" --ylab="Enriched Terms" --width 24 --height 18 --label_width 40 --format png --dpi 300 --no-rotate --verbose
Note: values passed to --xlab or --ylab that start with - should use --option=value syntax to avoid being parsed as flags.
Note: separator variants are supported only when they are passed inside a single --feature argument value.
Plot Input
- Plotting is triggered by
scripts/main.R --go_input: optional.rdafile containing aGO_listobject--kegg_input: optional.rdafile containing aKEGG_listobject- If not provided,
main.Ruses the newly generated files underoutput_dir/temp - Plotting requires result tables with at least
Descriptionandp.adjust
Output Files
| File Name | Format | Description |
|---|---|---|
temp/GO_df.csv | CSV | GO enrichment result table |
temp/GO_list.rda | RDA | Full GO enrichment object |
temp/KEGG_df.csv | CSV | KEGG enrichment result table |
temp/KEGG_list.rda | RDA | Full KEGG enrichment object |
plot/gokegg_dot_chart.pdf etc. | PDF/PNG/SVG | Combined GO/KEGG dot chart |
plot/gokegg_dot_chart_data.csv | CSV | Combined plotting table used for the figure |
plot/gokegg_dot_chart_data.rda | RDA | Plot bundle with plotting data and parameters |
session_info.txt | TXT | Runtime session information |
Error Handling
Common error codes and fixes:
SKILL_FILE_NOT_FOUND: Input file does not exist; check the path and permissionsSKILL_FILE_FORMAT_ERROR:.rdacannot be read or is malformed; regenerate upstream resultsSKILL_MISSING_COLUMNS: Result table is missingDescriptionorp.adjustSKILL_EMPTY_DATA: Input genes are empty after parsing, cannot be converted, or enrichment results are emptySKILL_INVALID_PARAMETER: Required parameter missing, unsupported species, or insufficient color countSKILL_PACKAGE_NOT_FOUND: Required package is not installedSKILL_ANALYSIS_FAILED: Internal GO/KEGG enrichment failure; verifygene_type,sp, and input genes
For detailed troubleshooting, read references/troubleshooting.md.
Testing
Minimal test dataset: use a small built-in gene list directly, with no extra files required.
Smoke test command:
Rscript scripts/main.R --feature "TP53,EGFR,BRCA1,MYC" --output_dir ./test_output --sp org.Hs.eg.db --gene_type SYMBOL --pvalue_cutoff 0.05 --qvalue_cutoff 0.2 --pAdjustMethod BH --seed 66 --go_top_n 3 --kegg_top_n 3 --format pdf --verbose
Expected smoke-test outputs:
./test_output/temp/GO_list.rda./test_output/temp/KEGG_list.rda./test_output/temp/GO_df.csv./test_output/temp/KEGG_df.csv./test_output/plot/gokegg_dot_chart.pdf./test_output/plot/gokegg_dot_chart_data.csv./test_output/plot/gokegg_dot_chart_data.rda./test_output/session_info.txt- Exit status code
0
Automated regression script:
Rscript test/test_regressions.R
The regression script covers:
- Separator parsing with comma, Chinese semicolon, newline, tab, and mixed separators
- Empty parsed-gene handling
- Invalid
--plot_marginvalidation - Plot input validation for missing GO/KEGG inputs
Separator examples for manual CLI verification:
Rscript scripts/main.R --feature "TP53,EGFR,BRCA1,MYC" --output_dir ./test_sep_comma
Rscript scripts/main.R --feature "TP53；EGFR；BRCA1；MYC" --output_dir ./test_sep_cn_semicolon
Rscript scripts/main.R --feature $'TP53\nEGFR\nBRCA1\nMYC' --output_dir ./test_sep_newline
Rscript scripts/main.R --feature $'TP53\tEGFR\tBRCA1\tMYC' --output_dir ./test_sep_tab
Rscript scripts/main.R --feature $'TP53； EGFR, BRCA1 MYC' --output_dir ./test_sep_mixed
Note: all separators must be passed inside a single --feature argument value.
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 11 other files (scripts, references, assets) in awesome-med-research-skills/Data Analysis/gokegg of aipoch/medical-research-skills.
- SKILL.md
- assets/KEGG_pathway_name.txt
- eval_report_gokegg_result.json
- references/algorithm.md
- references/cli-guide.md
- references/troubleshooting.md
- scripts/dochart.R
- scripts/functions.R
- scripts/main.R
- scripts/run_analysis.R
- scripts/utils.R
- test/data/gene.txt
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Gokegg Analysis 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 |
|---|---|---|---|---|---|---|
| Gokegg Analysis this skillaipoch/medical-research-skills | 1.9k | — | ~2.7k | Automated safety check: Pass | MIT | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Questions about Gokegg Analysis
What does Gokegg Analysis do?
A skill your agent uses when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart. Gokegg Analysis is an agent skill from aipoch/medical-research-skills. Use when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart.
When should I use Gokegg Analysis?
Gokegg Analysis fits situations like: performing GO and KEGG enrichment on a gene list from bulk RNA-seq; microarray studies; then generating a combined GO/KEGG dot chart.
How do I install Gokegg Analysis in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill gokegg-analysis -a claude-code`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/gokegg in aipoch/medical-research-skills) into .claude/skills/gokegg-analysis in your project. Claude Code loads it when a task matches its description.
How do I install Gokegg Analysis in Codex?
Run `npx skills add aipoch/medical-research-skills --skill gokegg-analysis -a codex`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/gokegg in aipoch/medical-research-skills) into .agents/skills/gokegg-analysis in your project. Codex loads it when a task matches its description.
Can I use Gokegg Analysis 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 aipoch/medical-research-skills --skill gokegg-analysis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gokegg-analysis, .gemini/skills/gokegg-analysis, .github/skills/gokegg-analysis and .opencode/skills/gokegg-analysis in your project.
What does Gokegg Analysis need to run?
Going by SKILL.md and its folder, Gokegg Analysis needs R for the scripts in its folder and the command-line tools its instructions call (go).
Does Gokegg Analysis access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Gokegg Analysis 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Gokegg Analysis use?
Gokegg Analysis is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Gokegg Analysis use?
About 2.7k tokens (SKILL.md is roughly 11k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 3.8k tokens, read only when the agent opens those files.
What are the alternatives to Gokegg Analysis?
Skills that share tags, products or a category with Gokegg Analysis: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Gokegg Analysis?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,937 GitHub stars. The repository holds 578 skills in this directory. The repository was last updated on September 17, 2026.
Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.