Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
A skill your agent uses when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap.
Install Deg Screening Analysis
$ npx skills add aipoch/medical-research-skills --skill deg-screening-analysis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills deg-screening-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/deg-screening-analysis' .claude/skills/deg-screening-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 "deg-screening-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/deg-screening-analysis into .claude/skills/deg-screening-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deg-screening-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/deg-screening-analysisType 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 deg-screening-analysis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills deg-screening-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/deg-screening-analysis' .agents/skills/deg-screening-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 "deg-screening-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/deg-screening-analysis into .agents/skills/deg-screening-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deg-screening-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 deg-screening-analysis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills deg-screening-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/deg-screening-analysis' .cursor/skills/deg-screening-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 "deg-screening-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/deg-screening-analysis into .cursor/skills/deg-screening-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deg-screening-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/deg-screening-analysis'--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 deg-screening-analysis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills deg-screening-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/deg-screening-analysis' .gemini/skills/deg-screening-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 "deg-screening-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/deg-screening-analysis into .gemini/skills/deg-screening-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deg-screening-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 deg-screening-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 deg-screening-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/deg-screening-analysis' .github/skills/deg-screening-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 "deg-screening-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/deg-screening-analysis into .github/skills/deg-screening-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deg-screening-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 deg-screening-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 deg-screening-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/deg-screening-analysis' .opencode/skills/deg-screening-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 "deg-screening-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/deg-screening-analysis into .opencode/skills/deg-screening-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deg-screening-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
deg-screening-analysis- GitHub stars
- 2k
- Token cost
- ~2.1k tokens
- SKILL.md length
- 884 words
- Files
- 14 (incl. scripts, references)
- Skills in repo
- 567
- Repo updated
- First seen
- Licence
- MIT
At a glance
A skill your agent uses when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap.
- Works in 4 steps: Validate Input → Run Differential Expression → Screen Differentially Expressed Genes → …
- Screening differentially expressed genes from a bulk expression matrix between two user-specified groups
- SKILL.md covers When to Use, Out of Scope, Practical Caveats and When to Read External Files, plus 6 more sections
- Runs R scripts from its folder
What it does
Deg Screening Analysis is an agent skill from aipoch/medical-research-skills. Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Triggers include DEG analysis, volcano plot, clustered heatmap, limma-based two-group comparison, and case-vs-control screening. NOT for single-cell RNA-seq, multi-group contrasts, count-model workflows such as DESeq2/edgeR, or non-expression omics data.
Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 17 other files, including scripts and reference files (for example `eval_report_deg-screening-analysis_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
- Screening differentially expressed genes from a bulk expression matrix between two user-specified groups
- Producing DEG tables
- A clustered heatmap
- Include DEG analysis
Example prompts
- “/deg-screening-analysis”
Workflow steps
4 steps, taken from the step headings in SKILL.md.
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 6 files in scripts/ (R), which the agent can run.
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
Deg Screening Analysis loads about 2.1k tokens when it runs, and up to ~5k if it reads all its reference files. Until then it costs about 114 tokens; SKILL.md has 884 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). 884 words, ~2,071 tokens.
Download SKILL.mdSave it as
.claude/skills/deg-screening-analysis/SKILL.md (or your agent's skills folder). This skill also uses 13 other files; get the full folder from GitHub.- name
- deg-screening-analysis
- description
- Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Triggers include DEG analysis, volcano plot, clustered heatmap, limma-based two-group comparison, and case-vs-control screening. NOT for single-cell RNA-seq, multi-group contrasts, count-model workflows such as DESeq2/edgeR, or non-expression omics data.
- license
- MIT
- author
- AIPOCH
Differential Expression Gene Screening Analysis (Volcano Plot & Clustered Heatmap)
When to Use
Use this skill when you need a reproducible two-group DEG workflow on a bulk expression matrix and want:
- a full differential expression table
- a filtered DEG table
- a volcano plot
- a clustered heatmap of top differential genes
Typical requests include:
- compare case vs control samples with limma
- screen upregulated and downregulated genes from a normalized expression matrix
- generate a DEG table with volcano and heatmap outputs from bulk transcriptome data
Out of Scope
Do not use this skill for:
- single-cell RNA-seq workflows
- multi-group contrasts or factorial designs
- count-model pipelines that require
DESeq2oredgeR - batch correction, covariate-adjusted models, or generalized design-matrix consulting
- non-expression omics data
If the request falls outside this scope, stop and hand off to a more appropriate analysis workflow instead of forcing the data through this skill.
Practical Caveats
Diffanalysis.csvcurrently exportsname,logFC,P.value, andP.adj.--p_typecontrols both DEG screening semantics and volcano plot significance semantics.plot/heatmap.pdfis generated only when at least two heatmap genes remain after ranking.- When the result is very sparse, prefer keeping tables and volcano output as the primary artifacts.
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details or statistical assumptions | references/algorithm.md | limma method, filtering logic, volcano/heatmap selection rules |
| Need to execute the workflow | scripts/main.R | Get the exact CLI entry and runnable command |
| Encounter an error code or bad input format | references/troubleshooting.md | Match SKILL_* errors to causes and fixes |
| Need more CLI examples | references/cli-guide.md | See complete command examples for common use cases |
| Need a minimal runnable example | tests/data/ | Use bundled test input files for validation |
Usage
Rscript scripts/main.R \
--input_file tests/data/oa_exp.csv \
--group_file tests/data/oa_group.csv \
--case OA \
--control control \
--output_dir ./resultsArguments
| Short | Long | Type | Default | Required | Description |
|---|---|---|---|---|---|
-i | --input_file | character | none | yes | Expression matrix CSV. First column is gene ID, remaining columns are sample values. |
-g | --group_file | character | none | yes | Group annotation CSV. The script auto-detects sample and group columns, including files where the first column is row names or index. |
-o | --output_dir | character | ./DEG | no | Output directory for tables, plots, and session metadata. |
| --case | character | none | yes | Case group name to compare. Matching is case-insensitive and trimmed. |
| --control | character | none | yes | Control group name to compare. Matching is case-insensitive and trimmed. |
-m | --diff_method | character | limma | no | Differential expression method. Current implementation supports limma only. |
-p | --p_threshold | numeric | 0.05 | no | Significance threshold for DEG screening. |
-f | --logfc_threshold | numeric | 1 | no | Absolute log fold change threshold for DEG screening. |
| --top_n | integer | 5 | no | Number of top upregulated and top downregulated genes considered for heatmap selection. |
| --p_type | character | p.adj | no | P-value field used for significance filtering and volcano significance coloring. Allowed values: p, p.adj. |
| --run_plots | logical | TRUE | no | Whether to generate the volcano plot and clustered heatmap. |
| --timeout_seconds | integer | 3600 | no | Maximum allowed runtime before timeout. |
-s | --seed | integer | 42 | no | Random seed recorded for reproducibility. |
Output Files
| File | Format | Description |
|---|---|---|
session_info.txt | txt | R session metadata and package versions used in the run. |
data/DEG_list.rda | rda | Serialized R object containing method, groups, thresholds, the full differential table, and the screened DEG table. |
table/Diffanalysis.csv | csv | Full differential expression result table with columns name, logFC, P.value, and P.adj. |
table/DEG.csv | csv | Significant DEG table only, containing screened genes with group labels up or down. |
plot/volcano_plot.pdf | Volcano plot of differential genes using the p-value mode selected by --p_type. | |
plot/heatmap.pdf | Clustered heatmap for selected top differential genes when at least two heatmap genes are available and plotting is enabled. |
Show full SKILL.md (316 more words)Show less
Workflow
Step 1: Validate Input
- check that input files exist
- load the expression matrix and ensure it is non-empty
- auto-detect sample and group columns in the group file
- verify sample IDs overlap correctly
- verify case/control groups exist and each selected group has at least two samples
Step 2: Run Differential Expression
- fit a two-group limma linear model
- build the contrast
case - control - compute empirical Bayes moderated statistics
- export the full differential result table
Step 3: Screen Differentially Expressed Genes
- apply
p_thresholdandlogfc_threshold - use
P.valueorP.adjbased on--p_type - label genes as
up,down, orno - export DEG tables and serialized result objects
Step 4: Generate Volcano Plot & Clustered Heatmap
- build
plot/volcano_plot.pdfdirectly from the full differential table - select top up and top down genes for heatmap input
- build
plot/heatmap.pdfonly when at least two heatmap genes are available
Error Handling
| Error Code | Meaning | Typical Fix |
|---|---|---|
SKILL_FILE_NOT_FOUND | Input file path does not exist | Verify the file path and rerun |
SKILL_PACKAGE_NOT_FOUND | Required R package is missing | Install the missing package, then rerun |
SKILL_MISSING_COLUMNS | Input file does not contain the necessary columns | Check CSV structure and column placement |
SKILL_EMPTY_DATA | Input file is empty or limma returns no analyzable rows | Validate input content or confirm the matrix contains enough valid values |
SKILL_INVALID_PARAMETER | Argument value or group selection is invalid | Check thresholds, --case, --control, and --p_type |
SKILL_SAMPLE_MISMATCH | Expression matrix samples and group file samples do not match | Align sample IDs between the two input files |
SKILL_TIMEOUT | The run exceeded the allowed runtime | Increase --timeout_seconds or simplify the run |
If you need step-by-step fixes, read references/troubleshooting.md.
Testing
Rscript tests/run_tests.RMinimal CLI smoke test:
Rscript scripts/main.R \
--input_file tests/data/oa_exp.csv \
--group_file tests/data/oa_group.csv \
--case OA \
--control control \
--output_dir ./tests_outputExpected outputs:
tests_output/table/Diffanalysis.csvtests_output/table/DEG.csvtests_output/plot/volcano_plot.pdftests_output/session_info.txt
tests_output/plot/heatmap.pdf is expected only when enough significant genes remain for heatmap rendering.
Runs with fewer than two selected heatmap genes skip heatmap generation with a warning instead of failing.
tests_output/table/DEG.csv may be empty when no genes pass the current thresholds.
Skill name: deg-screening-analysis
© 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 13 other files (scripts, references) in awesome-med-research-skills/Data Analysis/deg-screening-analysis of aipoch/medical-research-skills.
- SKILL.md
- eval_report_deg-screening-analysis_result.json
- references/algorithm.md
- references/cli-guide.md
- references/troubleshooting.md
- scripts/diff_methods.R
- scripts/diff_visualization.R
- scripts/functions.R
- scripts/main.R
- scripts/run_analysis.R
- scripts/utils.R
- tests/data/oa_exp.csv
- tests/data/oa_group.csv
- tests/run_tests.R
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Deg Screening 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 |
|---|---|---|---|---|---|---|
| Deg Screening Analysis this skillaipoch/medical-research-skills | 2k | — | ~2.1k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 3 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw | 15k | — | ~923 | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Deg Screening Analysis
What does Deg Screening Analysis do?
A skill your agent uses when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Deg Screening Analysis is an agent skill from aipoch/medical-research-skills. Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap.
When should I use Deg Screening Analysis?
Deg Screening Analysis fits situations like: screening differentially expressed genes from a bulk expression matrix between two user-specified groups; producing DEG tables; A clustered heatmap; include DEG analysis.
How do I install Deg Screening Analysis in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill deg-screening-analysis -a claude-code`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/deg-screening-analysis in aipoch/medical-research-skills) into .claude/skills/deg-screening-analysis in your project. Claude Code loads it when a task matches its description.
How do I install Deg Screening Analysis in Codex?
Run `npx skills add aipoch/medical-research-skills --skill deg-screening-analysis -a codex`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/deg-screening-analysis in aipoch/medical-research-skills) into .agents/skills/deg-screening-analysis in your project. Codex loads it when a task matches its description.
Can I use Deg Screening 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 deg-screening-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/deg-screening-analysis, .gemini/skills/deg-screening-analysis, .github/skills/deg-screening-analysis and .opencode/skills/deg-screening-analysis in your project.
What does Deg Screening Analysis need to run?
Going by SKILL.md and its folder, Deg Screening Analysis needs R for the scripts in its folder.
Does Deg Screening 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 Deg Screening 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 Deg Screening Analysis use?
Deg Screening 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 Deg Screening Analysis use?
About 2.1k tokens (SKILL.md is roughly 8.3k 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 2.9k tokens, read only when the agent opens those files.
What are the alternatives to Deg Screening Analysis?
Skills that share tags, products or a category with Deg Screening Analysis: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Deg Screening Analysis?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 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.