Bio Outlier Splicing Detection
GPTomics/bioSkills
Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q…
Blood RNA-seq expression-outlier detection for rare-disease diagnostics.
Install Rare Disease Rnaseq
$ npx skills add ClawBio/ClawBio --skill rare-disease-rnaseq -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install ClawBio/ClawBio rare-disease-rnaseq --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/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/rare-disease-rnaseq .claude/skills/rare-disease-rnaseq && 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 "rare-disease-rnaseq" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/rare-disease-rnaseq into .claude/skills/rare-disease-rnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "rare-disease-rnaseq", 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/ClawBio/ClawBio/tree/main/skills/rare-disease-rnaseqType 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 ClawBio/ClawBio --skill rare-disease-rnaseq -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install ClawBio/ClawBio rare-disease-rnaseq --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/rare-disease-rnaseq .agents/skills/rare-disease-rnaseq && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "rare-disease-rnaseq" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/rare-disease-rnaseq into .agents/skills/rare-disease-rnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "rare-disease-rnaseq", 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 ClawBio/ClawBio --skill rare-disease-rnaseq -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install ClawBio/ClawBio rare-disease-rnaseq --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/rare-disease-rnaseq .cursor/skills/rare-disease-rnaseq && 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 "rare-disease-rnaseq" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/rare-disease-rnaseq into .cursor/skills/rare-disease-rnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "rare-disease-rnaseq", 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/ClawBio/ClawBio.git --path skills/rare-disease-rnaseq--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 ClawBio/ClawBio --skill rare-disease-rnaseq -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install ClawBio/ClawBio rare-disease-rnaseq --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/rare-disease-rnaseq .gemini/skills/rare-disease-rnaseq && 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 "rare-disease-rnaseq" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/rare-disease-rnaseq into .gemini/skills/rare-disease-rnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "rare-disease-rnaseq", 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 ClawBio/ClawBio rare-disease-rnaseqInstalls 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 ClawBio/ClawBio --skill rare-disease-rnaseq -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/rare-disease-rnaseq .github/skills/rare-disease-rnaseq && 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 "rare-disease-rnaseq" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/rare-disease-rnaseq into .github/skills/rare-disease-rnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "rare-disease-rnaseq", 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 ClawBio/ClawBio --skill rare-disease-rnaseq -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install ClawBio/ClawBio rare-disease-rnaseq --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/rare-disease-rnaseq .opencode/skills/rare-disease-rnaseq && 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 "rare-disease-rnaseq" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/rare-disease-rnaseq into .opencode/skills/rare-disease-rnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "rare-disease-rnaseq", 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
rare-disease-rnaseq- GitHub stars
- 1.2k
- Used in
- 1 other repo
- Token cost
- ~1.2k tokens
- SKILL.md length
- 396 words
- Files
- 4
- Skills in repo
- 104
- Repo updated
- First seen
- Licence
- MIT
At a glance
Blood RNA-seq expression-outlier detection for rare-disease diagnostics.
- Works in 5 steps: Library-size normalise (CPM),… → For each gene: compute median and MAD… → For each case-gene cell: modified z =… → …
- Tasks that involve Bioinformatics
- SKILL.md covers When To Use, Method, Input Contract and Output Structure, plus 4 more sections
- Runs Python scripts from its folder; calls python
What it does
Rare Disease Rnaseq is an agent skill from ClawBio/ClawBio. Blood RNA-seq expression-outlier detection for rare-disease diagnostics. Cases scored against a control reference panel; outliers ranked and filtered by a haploinsufficient disease-gene panel.
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files (for example `rare_disease_rnaseq.py` and `tests/test_rare_disease_rnaseq.py`).
It sits in Research & Science, covering Bioinformatics and Data cleaning. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve Data cleaning
Example prompts
- “/rare-disease-rnaseq”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Library-size normalise (CPM), log-transform
- For each gene: compute median and MAD across the control panel
- For each case-gene cell: modified z = 0.6745 (x − median) / MAD
- Flag |z| ≥ threshold (default 3) and gene in disease panel
- Rank by |z|, separate down-outliers (haploinsufficiency-consistent) from up-outliers
What it can do on your machine
Read from SKILL.md and the folder at commit dece754. 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 script files (Python), which the agent can run.
Shell commands in SKILL.md call:
python
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
Rare Disease Rnaseq loads about 1.2k tokens when it runs. Until then it costs about 53 tokens; SKILL.md has 396 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
The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 396 words, ~1,231 tokens.
Download SKILL.mdSave it as
.claude/skills/rare-disease-rnaseq/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- rare-disease-rnaseq
- description
- Blood RNA-seq expression-outlier detection for rare-disease diagnostics. Cases scored against a control reference panel; outliers ranked and filtered by a haploinsufficient disease-gene panel.
- license
- MIT
- metadata.tags
- rna-seq, rare-disease, outlier-detection, OUTRIDER, FRASER, diagnostic, blood, transcriptomics, haploinsufficiency
- metadata.trigger_keywords
- rare disease rnaseq, expression outlier, OUTRIDER, FRASER, blood rna-seq diagnostic, NGRL, undiagnosed, candidate diagnosis
- metadata.version
- 0.1.0
🩸 Rare-Disease Blood RNA-seq Outlier Detection
Reproduces the diagnostic principle of the Genomics England NGRL paper (Blood-based RNA-Seq of 5,412 individuals, medRxiv 2026.03.19.26348811). For each case sample, scores per-gene expression against a control reference panel and flags candidates falling in a curated dosage-sensitive disease-gene panel.
When To Use
- A WGS-negative or WGS-VUS rare-disease patient with a paired blood RNA-seq sample
- A clinical bioinformatician triaging candidate diagnoses before MDT review
- A population-biobank team building an ancestry-matched control reference for outlier calling (e.g. Qatar Biobank for Sidra paediatric cases)
Method
Per-gene robust outlier scoring on log2(CPM+1):
- Library-size normalise (CPM), log-transform
- For each gene: compute median and MAD across the control panel
- For each case-gene cell: modified z = 0.6745 (x − median) / MAD
- Flag |z| ≥ threshold (default 3) and gene in disease panel
- Rank by |z|, separate down-outliers (haploinsufficiency-consistent) from up-outliers
This implements the diagnostic principle of OUTRIDER (per-gene outlier vs control panel) without the autoencoder, so it runs in seconds with no R/Bioconductor stack. For clinical-grade calls swap to the full DROP pipeline (gagneurlab/drop) which adds OUTRIDER's denoising autoencoder, FRASER2 splicing outliers, and confounder correction. The skill's I/O contract is the same so the upgrade is drop-in.
Input Contract
- Counts matrix (
.csvor.tsv): rows = genes (HGNC symbol), columns = sample IDs - Cases file (
.txt): one case sample ID per line - Controls file (
.txt): one control sample ID per line (typically n ≥ 50) - Disease panel (optional,
.csvwithgeneandmechanismcolumns): defaults to a built-in 50-gene haploinsufficient panel
Show full SKILL.md (147 more words)Show less
Output Structure
rdoutlier_report/
├── report.md # per-case candidate diagnoses + clinical narrative
├── result.json # standard ClawBio envelope
├── figures/
│ └── case_outlier_heatmap.png # z-scores across cases × top genes
├── tables/
│ ├── outlier_calls.csv # all flagged outliers with z-score, direction, mechanism
│ └── per_gene_stats.csv # control median + MAD per gene
└── reproducibility/
├── commands.sh
├── environment.yml
└── checksums.sha256Demo
python clawbio.py run rdoutlier --demoGenerates 100 synthetic Gulf-ancestry control samples + 2 cases with injected outliers (FBN1 down, NF1 up) across a 200-gene panel. Demonstrates the diagnostic loop end-to-end in seconds.
Production Path (Sidra / QBB Reference)
| Component | Demo | Production |
|---|---|---|
| Aligner + quantifier | none (synthetic counts) | STAR + featureCounts (or Salmon) |
| Outlier algorithm | robust per-gene z-score | OUTRIDER autoencoder + FRASER2 splicing |
| Control panel | 100 synthetic samples | QBB n≈12K PAXgene blood RNA-seq |
| Confounder correction | none | DROP pipeline (RIN, batch, hidden factors) |
| Disease panel | 50 haploinsufficient genes | ClinGen haploinsufficient + PanelApp |
| Return-of-result loop | report.md | Sidra MDT reflex from WGS-negative referrals |
Safety
- Local-only processing, no network calls in core pipeline
- Compatible with secure research environments (Genomics England RE pattern; Sidra clinical genomics environment)
- Disclaimer required on every report
Disclaimer
ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.
© ClawBio, 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 3 other files in skills/rare-disease-rnaseq of ClawBio/ClawBio.
- SKILL.md
- data/disease_panel.csv
- rare_disease_rnaseq.py
- tests/test_rare_disease_rnaseq.py
Open the folder on GitHubat commit dece754
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Rare Disease Rnaseq 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 |
|---|---|---|---|---|---|---|
| Rare Disease Rnaseq this skillClawBio/ClawBio | 1.2k | 1 repos | ~1.2k | Automated safety check: Pass | MIT | |
| Bio Outlier Splicing DetectionGPTomics/bioSkills | 1.2k | 2 repos | ~5.1k | Automated safety check: Pass | MIT | |
| Bio Proteomics Data ImportFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.2k | Automated safety check: Pass | None | |
| Bio Splicing QcGPTomics/bioSkills | 1.2k | 2 repos | ~6.2k | Automated safety check: Pass | MIT | |
| Knn Imputationaipoch/medical-research-skills | 1.9k | — | ~2.5k | Automated safety check: Pass | MIT | |
| Bio Proteomics Proteomics QcFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.8k | Automated safety check: Pass | None |
Similar skills
Bio Proteomics Data Import
FreedomIntelligence/OpenClaw-Medical-Skills
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt.
Bio Splicing Qc
GPTomics/bioSkills
Assesses RNA-seq data quality specifically for alternative splicing analysis.
Knn Imputation
aipoch/medical-research-skills
A skill your agent uses when filtering genes with high missingness and then imputing missing values in a bulk expression matrix with group-aware KNN through DMwR2, where donor samples are restricted…
Bio Proteomics Proteomics Qc
FreedomIntelligence/OpenClaw-Medical-Skills
Quality control and assessment for proteomics data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
Bio Workflows Methylation Pipeline
GPTomics/bioSkills
Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation…
More from ClawBio/ClawBio
All 104 skills in this repoEqtl Catalogue Region Fetch
ClawBio/ClawBio
Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP.
Xena Tcga Gene Query
ClawBio/ClawBio
Query TCGA tumor biology through the ucscxenatoolspy API. An agent skill from ClawBio/ClawBio.
Gwas Catalog Region Fetch
ClawBio/ClawBio
Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP.
Dnasp
ClawBio/ClawBio
Population genetics of pre-aligned DNA sequences or multi-sample VCFs using selected DnaSP 6 methods.
Ld 1000g Region Compute
ClawBio/ClawBio
Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified.
Ncbi Datasets
ClawBio/ClawBio
Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
Related
Categories
Questions about Rare Disease Rnaseq
What does Rare Disease Rnaseq do?
Blood RNA-seq expression-outlier detection for rare-disease diagnostics. Rare Disease Rnaseq is an agent skill from ClawBio/ClawBio. Blood RNA-seq expression-outlier detection for rare-disease diagnostics.
When should I use Rare Disease Rnaseq?
Rare Disease Rnaseq fits situations like: tasks that involve Bioinformatics; tasks that involve Data cleaning.
How do I install Rare Disease Rnaseq in Claude Code?
Run `npx skills add ClawBio/ClawBio --skill rare-disease-rnaseq -a claude-code`. Or copy the skill folder (skills/rare-disease-rnaseq in ClawBio/ClawBio) into .claude/skills/rare-disease-rnaseq in your project. Claude Code loads it when a task matches its description.
How do I install Rare Disease Rnaseq in Codex?
Run `npx skills add ClawBio/ClawBio --skill rare-disease-rnaseq -a codex`. Or copy the skill folder (skills/rare-disease-rnaseq in ClawBio/ClawBio) into .agents/skills/rare-disease-rnaseq in your project. Codex loads it when a task matches its description.
Can I use Rare Disease Rnaseq 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 ClawBio/ClawBio --skill rare-disease-rnaseq -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/rare-disease-rnaseq, .gemini/skills/rare-disease-rnaseq, .github/skills/rare-disease-rnaseq and .opencode/skills/rare-disease-rnaseq in your project.
What does Rare Disease Rnaseq need to run?
Going by SKILL.md and its folder, Rare Disease Rnaseq needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Rare Disease Rnaseq 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 Rare Disease Rnaseq 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 Rare Disease Rnaseq use?
Rare Disease Rnaseq 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 Rare Disease Rnaseq use?
About 1.2k tokens (SKILL.md is roughly 4.9k 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 Rare Disease Rnaseq?
Skills that share tags, products or a category with Rare Disease Rnaseq: Bio Outlier Splicing Detection (GPTomics/bioSkills, 1.2k stars), Bio Proteomics Data Import (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Splicing Qc (GPTomics/bioSkills, 1.2k stars) and Knn Imputation (aipoch/medical-research-skills, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Rare Disease Rnaseq?
ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,155 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 9, 2026.
Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.