Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
A skill your agent uses when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization.
$ npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills consensus-clustering-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/consensus-clustering-analysis' .claude/skills/consensus-clustering-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 "consensus-clustering-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/consensus-clustering-analysis into .claude/skills/consensus-clustering-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-clustering-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/consensus-clustering-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 consensus-clustering-analysis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills consensus-clustering-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/consensus-clustering-analysis' .agents/skills/consensus-clustering-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 "consensus-clustering-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/consensus-clustering-analysis into .agents/skills/consensus-clustering-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-clustering-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 consensus-clustering-analysis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills consensus-clustering-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/consensus-clustering-analysis' .cursor/skills/consensus-clustering-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 "consensus-clustering-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/consensus-clustering-analysis into .cursor/skills/consensus-clustering-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-clustering-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/consensus-clustering-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 consensus-clustering-analysis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills consensus-clustering-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/consensus-clustering-analysis' .gemini/skills/consensus-clustering-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 "consensus-clustering-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/consensus-clustering-analysis into .gemini/skills/consensus-clustering-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-clustering-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 consensus-clustering-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 consensus-clustering-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/consensus-clustering-analysis' .github/skills/consensus-clustering-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 "consensus-clustering-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/consensus-clustering-analysis into .github/skills/consensus-clustering-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-clustering-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 consensus-clustering-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 consensus-clustering-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/consensus-clustering-analysis' .opencode/skills/consensus-clustering-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 "consensus-clustering-analysis" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/consensus-clustering-analysis into .opencode/skills/consensus-clustering-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-clustering-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.
consensus-clustering-analysisA skill your agent uses when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization.
Consensus Clustering Analysis is an agent skill from aipoch/medical-research-skills. Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables.
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 24 other files, including scripts and reference files (for example `eval_report_consensus-clustering-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.
4 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.
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.
Ships 6 files in scripts/ (R, from the files we listed), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Consensus Clustering Analysis loads about 2k tokens when it runs, and up to ~6.1k if it reads all its reference files. Until then it costs about 77 tokens; SKILL.md has 671 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.
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.
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 671 words, ~1,966 tokens.
.claude/skills/consensus-clustering-analysis/SKILL.md (or your agent's skills folder). This skill also uses 20 other files; get the full folder from GitHub.Use this skill when you need to identify stable sample subtypes from a bulk expression matrix with ConsensusClusterPlus, compare candidate clustering settings with PAC, and export consensus matrix/CDF visualizations.
Do not use this skill for differential expression analysis, single-cell clustering, or non-expression tabular data.
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md | Consensus clustering, PAC scoring, and preprocessing assumptions |
| Need to run analysis | scripts/main.R | Execute: Rscript scripts/main.R --input_file ... --group_file ... |
| Encounter errors | references/troubleshooting.md | Common errors and solutions |
| Need CLI examples | references/cli-guide.md | Detailed CLI usage examples with verified local runs |
Rscript scripts/main.R \
--input_file ./expression_matrix.csv \
--group_file ./groups.csv \
--disease_group case \
--max_k 4 \
--output_dir ./output/ \
--gene_selection highly_variable \
--top_n 5000 \
--reps 1000 \
--p_item 0.8 \
--p_feature 1.0 \
--timeout_seconds 3600 \
--seed 42| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-i | --input_file | character | required | Expression matrix file (genes as rows, samples as columns) |
-g | --group_file | character | required | Group information file (sample ID + group columns) |
-d | --disease_group | character | case | Group label retained for clustering |
-k | --max_k | integer | 4 | Maximum cluster count to evaluate |
-o | --output_dir | character | ./output/ | Output directory |
-m | --gene_selection | character | highly_variable | Gene selection mode: highly_variable or custom |
-n | --top_n | integer | 5000 | Number of top variable genes to keep |
-l | --gene_list | character | NULL | Custom gene list file when gene_selection=custom |
-c | --center_data | logical | TRUE | Median-center each gene before clustering |
-r | --reps | integer | 1000 | Consensus resampling repetitions |
--p_item | double | 0.8 | Sample resampling proportion | |
--p_feature | double | 1.0 | Feature resampling proportion | |
-t | --timeout_seconds | integer | 3600 | Elapsed timeout in seconds |
-s | --seed | integer | 42 | Random seed for reproducibility |
Genes as rows, samples as columns, CSV/TSV/TXT format with gene ID in the first column.
,Sample01,Sample02,Sample03
TSPAN6,1.8479,1.8318,3.8276
TNMD,0.0349,0.0533,1.3889Delimited text file with sample ID and group columns.
sample,group
Sample01,case
Sample02,control
Sample03,caseOptional plain text or single-column CSV file with one gene symbol per line.
TNMD
DPM1
SCYL3| File | Description |
|---|---|
Cluster_res.csv | PAC summary for each distance/algorithm combination with is_best marking the selected model |
genes_for_clustering.csv | Selected genes and gene selection mode |
samples_for_clustering.csv | Samples retained after disease-group filtering |
result_<distance>_<algorithm>/ | Method-specific consensus outputs and PAC_scores.csv |
Consensus Matrix Plot.pdf | Consensus matrix heatmap for the optimal model |
CDF curve Plot.pdf | CDF curves for the optimal method |
session_info.txt | R session and package version info |
highly_variable or customRepeated subsampling is used to estimate cluster stability across candidate K values and clustering settings.
The proportion of ambiguous clustering is computed as CDF(0.9) - CDF(0.1) from lower-triangle consensus values. Lower PAC indicates more stable clustering.
highly_variable: rank genes by median absolute deviationcustom: use the intersection of the provided gene list and matrix row namesRscript scripts/main.R \
-i expression_matrix.csv \
-g groups.csv \
-d case \
-k 3 \
-r 20 \
-o output/example_basic \
-t 120Rscript scripts/main.R \
-i expression_matrix.csv \
-g groups.csv \
-d case \
-m custom \
-l genes.csv \
-k 4 \
-r 20 \
-o output/example_custom \
-t 120Rscript scripts/main.R \
-i expression_matrix.csv \
-g groups.csv \
-d case \
-c FALSE \
-k 3 \
-r 20 \
-o output/example_rawscale \
-t 120| Error | Cause | Solution |
|---|---|---|
SKILL_FILE_NOT_FOUND | Input file does not exist | Check file path and permissions |
SKILL_MISSING_COLUMNS | Group file lacks sample/group columns | Verify column names in the group file |
SKILL_SAMPLE_MISMATCH | Sample names do not match | Ensure group file sample IDs match matrix columns |
SKILL_INVALID_PARAMETER | CLI value is invalid | Check allowed options and numeric ranges |
SKILL_INVALID_DATA | Too few samples/genes remain after filtering | Lower max_k or review the input data |
SKILL_TIMEOUT | Run exceeded the configured timeout | Increase timeout_seconds or reduce reps |
SKILL_DEPENDENCY_MISSING | Required R package is not installed | Install missing packages before rerunning |
IF error persists, READ: references/troubleshooting.md
# Check help
Rscript scripts/main.R --help
# Run analysis
Rscript scripts/main.R \
-i tests/data/expression_matrix.csv \
-g tests/data/groups.csv \
-d case \
-k 3 \
-r 20 \
-o output/example_basic \
-t 120# Inspect selected model
cat output/example_basic/Cluster_res.csv
# Check output plots exist
ls -la output/example_basicoptparseset.seed() for reproducibilityrequireNamespace() dependency checksdata.table::fread() input readingSKILL.mdSKILL_* codesscripts/ directoryreferences/ directoryLast updated: 2026-04-17 | Version: 1.0.0
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 20 other files (scripts, references) in awesome-med-research-skills/Data Analysis/consensus-clustering-analysis of aipoch/medical-research-skills.
Open the folder on GitHubat commit 686e09d
Consensus Clustering 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 |
|---|---|---|---|---|---|---|
| Consensus Clustering Analysis this skillaipoch/medical-research-skills | 2k | — | ~2k | Automated safety check: Pass | MIT | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 16 repos | ~2.8k | Automated safety check: Pass | MIT | |
| deepTools NGS Toolkitdavila7/claude-code-templates | 32k | 13 repos | ~4.5k | Automated safety check: Pass | MIT | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 32k | 12 repos | ~4k | Automated safety check: Pass | MIT | |
| Gtars Genomic Interval Toolkitdavila7/claude-code-templates | 32k | 12 repos | ~1.9k | Automated safety check: Pass | MIT | |
| LaminDB Biological Data Managementdavila7/claude-code-templates | 32k | 12 repos | ~3.6k | Automated safety check: Pass | MIT |
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
davila7/claude-code-templates
Guides use of deepTools on sequencing data: BAM to bigWig conversion, QC, sample correlation, and heatmaps or profiles around TSS and peaks for ChIP-seq, RNA-seq and ATAC-seq.
davila7/claude-code-templates
Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
davila7/claude-code-templates
Works with genomic intervals using gtars, a Rust toolkit with Python bindings: overlap detection, coverage tracks, tokenization for ML models and reference sequences.
davila7/claude-code-templates
Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.
LigphiDonk/Oh-my--paper
Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.
aipoch/medical-research-skills
Complete workflow for generating academic research posters from PDF literature; use when you need to extract paper content from PDFs and produce a LaTeX-based poster…
aipoch/medical-research-skills
Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool.
aipoch/medical-research-skills
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
aipoch/medical-research-skills
A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS.
aipoch/medical-research-skills
Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…
aipoch/medical-research-skills
Creates academic-poster writing packages for LaTeX using beamerposter, tikzposter, or baposter.
Categories
A skill your agent uses when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. Consensus Clustering Analysis is an agent skill from aipoch/medical-research-skills. Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization.
Consensus Clustering Analysis fits situations like: identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus; including PAC-based model selection and consensus matrix/CDF visualization.
Run `npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -a claude-code`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/consensus-clustering-analysis in aipoch/medical-research-skills) into .claude/skills/consensus-clustering-analysis in your project. Claude Code loads it when a task matches its description.
Run `npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -a codex`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/consensus-clustering-analysis in aipoch/medical-research-skills) into .agents/skills/consensus-clustering-analysis in your project. Codex loads it when a task matches its description.
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 consensus-clustering-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/consensus-clustering-analysis, .gemini/skills/consensus-clustering-analysis, .github/skills/consensus-clustering-analysis and .opencode/skills/consensus-clustering-analysis in your project.
Going by SKILL.md and its folder, Consensus Clustering Analysis needs R for the scripts in its folder.
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.
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.
Consensus Clustering Analysis is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 2k tokens (SKILL.md is roughly 7.9k 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 4.1k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Consensus Clustering Analysis: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), deepTools NGS Toolkit (davila7/claude-code-templates, 32k stars), PyDESeq2 Differential Expression (davila7/claude-code-templates, 32k stars) and Gtars Genomic Interval Toolkit (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,973 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.