Content Research Writer
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
Load when biologically interpreting a finished verified consensus run (consensus-domains / sc-consensus-clustering) — inline DE, marker-DB lookup, and LLM cell-type naming with mandatory marker…
$ npx skills add TianGzlab/OmicsClaw --skill consensus-interpret -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw consensus-interpret --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/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/spatial/consensus-interpret .claude/skills/consensus-interpret && 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-interpret" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/consensus-interpret into .claude/skills/consensus-interpret/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-interpret", 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/TianGzlab/OmicsClaw/tree/main/skills/spatial/consensus-interpretType 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 TianGzlab/OmicsClaw --skill consensus-interpret -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw consensus-interpret --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/spatial/consensus-interpret .agents/skills/consensus-interpret && 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-interpret" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/consensus-interpret into .agents/skills/consensus-interpret/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-interpret", 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 TianGzlab/OmicsClaw --skill consensus-interpret -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw consensus-interpret --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/spatial/consensus-interpret .cursor/skills/consensus-interpret && 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-interpret" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/consensus-interpret into .cursor/skills/consensus-interpret/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-interpret", 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/TianGzlab/OmicsClaw.git --path skills/spatial/consensus-interpret--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 TianGzlab/OmicsClaw --skill consensus-interpret -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw consensus-interpret --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/spatial/consensus-interpret .gemini/skills/consensus-interpret && 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-interpret" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/consensus-interpret into .gemini/skills/consensus-interpret/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-interpret", 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 TianGzlab/OmicsClaw consensus-interpretInstalls 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 TianGzlab/OmicsClaw --skill consensus-interpret -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/spatial/consensus-interpret .github/skills/consensus-interpret && 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-interpret" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/consensus-interpret into .github/skills/consensus-interpret/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-interpret", 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 TianGzlab/OmicsClaw --skill consensus-interpret -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install TianGzlab/OmicsClaw consensus-interpret --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/spatial/consensus-interpret .opencode/skills/consensus-interpret && 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-interpret" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/consensus-interpret into .opencode/skills/consensus-interpret/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "consensus-interpret", 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-interpretLoad when biologically interpreting a finished verified consensus run (consensus-domains / sc-consensus-clustering) — inline DE, marker-DB lookup, and LLM cell-type naming with mandatory marker…
Consensus Interpret is an agent skill from TianGzlab/OmicsClaw. Load when biologically interpreting a finished verified consensus run (consensus-domains / sc-consensus-clustering) — inline DE, marker-DB lookup, and LLM cell-type naming with mandatory marker citations + evidence-bound next-step recommendations. Skip when the consensus run failed (fix it first); forward query→skill routing (use orchestrator).
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 37 other files, including reference files (for example `IMPLEMENTATION_PLAN.md`, `_artifacts.py` and `_candidates.py`).
It sits in Research & Science, covering Citation management. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is Apache-2.0.
Read from SKILL.md and the folder at commit 6fbd79f. 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 script files (Python, 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 Interpret loads about 2k tokens when it runs, and up to ~3.2k if it reads all its reference files. Until then it costs about 92 tokens; SKILL.md has 456 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); files beside SKILL.md are not scanned.
The full file from TianGzlab/OmicsClaw at commit 6fbd79f, republished under its Apache-2.0 licence (© TianGzlab). 456 words, ~1,962 tokens.
.claude/skills/consensus-interpret/SKILL.md (or your agent's skills folder). This skill also uses 35 other files; get the full folder from GitHub.The user has just finished a verified typed consensus run
(consensus-domains or sc-consensus-clustering) and wants the next
manual step (read cross_method_nmi.csv → run spatial-de →
cross-reference markers → name cell types → decide downstream skill) done
automatically with falsifiable evidence binding every LLM claim.
This skill does NOT replace the typed run. It is a strictly downstream
consumer: it reads <typed_run_dir>/{plan.json, consensus_labels.tsv, member_scores.csv, cross_method_nmi.csv} plus the original adata, and
writes its output to a different directory under
analysis://interpreted/<typed_run_id>. The verified-vs-exploratory
boundary established by ADR 0010 is preserved.
Skip when:
consensus_labels.tsv (i.e.
consensus-domains exited non-zero — fix the typed run first).query → skill dispatcher; use
orchestrator for that (forward direction).<!-- AUTO-GENERATED from skill.yaml (interface) — do not edit by hand. Regenerate: python scripts/generate_skill_md.py <skill_dir> -->
Inputs
directory.jsonOutputs
interpreted_report.mdinterpreted_assignments.jsonde_per_cluster.csvcontradiction_regions.csvaudit.json1. Preflight (T1 — fail-fast if any fail)
├─ Load plan.json from --input; assert schema_version + typed run integrity
├─ Locate adata at plan.json.input_path (or --adata override); check exists
├─ Load consensus_labels.tsv; assert observation column ⊆ adata.obs.index
├─ Resolve marker DB:
│ --markers <path> if given;
│ else bundled `data/markers/panglaodb_<tissue>.tsv` for --tissue;
│ else exit 5 (MarkerDBUnavailable)
└─ If LLM required and unreachable AND --no-llm not set → exit 6 (LLMUnavailable)
2. Per-cluster differential expression (deterministic, scanpy)
└─ scanpy.tl.rank_genes_groups(adata, groupby=consensus_<operator>, method='wilcoxon')
→ de_per_cluster.csv with top-K markers per cluster (K=20 default)
3. Marker → cell-type lookup (deterministic, pre-LLM)
└─ For each cluster, compute candidate cell types by ranking DB entries
whose gene appears in the cluster's top-K markers (weighted by db.weight × 1/de_rank).
4. LLM grounded interpretation (γ + β; one call per cluster + one synthesis call)
├─ Prompt template embeds (per cluster):
│ cluster_id, n_cells, top-K DE markers,
│ DB candidate cell types (ranked),
│ member_agreement summary, cross_method_nmi neighbors
├─ LLM must return JSON conforming to interpreted_assignments.json
│ schema; mandatory evidence.markers[] with non-empty
│ {gene, db_source, db_celltype}
└─ After all clusters: one synthesis call to produce next_steps[]
with mandatory evidence_refs[] (capped at top-3 by priority)
5. Invariant enforcement (T3 — fail-fast if violated)
├─ Every cluster.evidence.markers != [] → else exit 7
├─ Every next_steps[*].evidence_refs != [] → else exit 7
└─ Banner present and matches one of two allowed values → else exit 7
6. Coverage check (T2 — escalate to T1 if floor breached)
└─ interpretable_cluster_frac < --coverage-floor → exit 8
7. Artifact writes
├─ interpreted_report.md (banner enforced in format_interpreted_report)
├─ interpreted_assignments.json
├─ de_per_cluster.csv
├─ contradiction_regions.csv
└─ audit.jsonevidence.markers[] and
every next-step's evidence_refs[] must be non-empty, or the run exits 7
(InvariantViolation). Ungrounded LLM output is rejected, not silently kept.--no-llm changes the banner, not just the content. Structural-only mode
emits [I-noLLM: ...] and drops all cell-type claims; downstream consumers
must branch on the banner, not assume biology is present.analysis://interpreted/<run_id>, never overwriting the verified
analysis://typed/<run_id> evidence base (the ADR 0010 boundary).| Exit | Name | Meaning |
|---|---|---|
| 0 | success | All clusters interpreted (or low_confidence), invariants intact, no degradation triggered |
| 2 | argparse | CLI error |
| 3 | TypedRunInvalid | plan.json missing / malformed / not from a typed run |
| 4 | AdataMismatch | adata obs index disjoint from consensus_labels.tsv observation |
| 5 | MarkerDBUnavailable | --tissue not in bundled DBs and --markers not provided |
| 6 | LLMUnavailable | LLM endpoint unreachable and --no-llm not given |
| 7 | InvariantViolation | LLM violated marker-grounding or evidence-ref contract (T3) |
| 8 | CoverageBelowThreshold | < 50% of clusters interpretable (after T2 degradation) |
oc run consensus-domains --input preprocessed.h5ad --output run1/ \
--members banksy,graphst,leiden:resolution=0.5,leiden:resolution=1.0 \
--non-interactive --operator kmode --seed 0
oc run consensus-interpret --input run1/ --output run1_interpreted/ \
--tissue brain
# → run1_interpreted/interpreted_report.md begins with [A+I: ...]oc run consensus-interpret --input run1/ --output run1_struct/ \
--tissue brain --no-llm
# → run1_struct/interpreted_report.md begins with [I-noLLM: ...]
# → no cell-type claims, only cluster sizes / NMI summary / contradiction regionsoc run consensus-interpret --input run1/ --output run1_interp/ \
--markers ~/markers/mouse_intestine.tsv
# → bypasses --tissue requirement; uses user's custom DBreferences/methodology.md — the γ (naming) + β (recommendation) protocol and grounding rulesreferences/output_contract.md — interpreted_assignments.json schema + the 5 written artifactsreferences/parameters.md — every CLI flag (generated from skill.yaml)consensus-domains / sc-consensus-clustering (upstream — produce the verified run this interprets), orchestrator (sibling — forward query → skill; this does backward result → skill+evidence), spatial-de / spatial-deconv / spatial-communication (downstream — next-step skills β may recommend, each with mandatory evidence)© TianGzlab, Apache-2.0. 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 35 other files (references) in skills/spatial/consensus-interpret of TianGzlab/OmicsClaw.
Open the folder on GitHubat commit 6fbd79f
Consensus Interpret 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 Interpret this skillTianGzlab/OmicsClaw | 161 | — | ~2k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| NetworkxzLanqing/codex-claude-academic-skills | 4.6k | 16 repos | ~3.2k | Automated safety check: Pass | BSD-3-Clause | |
| Citation Verification GuideGalaxy-Dawn/claude-scholar | 5.7k | 3 repos | ~1.9k | Automated safety check: Pass | MIT | |
| Systematic Review ScreenerImbad0202/academic-research-skills | 51k | — | ~8.4k | Automated safety check: Pass | Custom licence | |
| Literature Reviewneflibata-feng/MyArxiv-Agent | 126 | 21 repos | ~5.9k | Automated safety check: Notes | MIT |
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
zLanqing/codex-claude-academic-skills
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python.
Galaxy-Dawn/claude-scholar
Reference guidance for checking every citation in academic writing against canonical sources such as DOI, arXiv, CrossRef and Semantic Scholar, to catch fake or wrong references.
Imbad0202/academic-research-skills
Screens records for systematic, scoping and rapid reviews against fixed eligibility rules, using two blinded AI reviewers and a third adjudicator, with traceable PRISMA counts.
neflibata-feng/MyArxiv-Agent
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
neflibata-feng/MyArxiv-Agent
Query and analyze scholarly literature using the OpenAlex database.
TianGzlab/OmicsClaw
Load when removing batch effects from a multi-cohort bulk RNA-seq dataset using ComBat (R or Python implementation).
TianGzlab/OmicsClaw
Load when discovering gene co-expression modules and hub genes in a bulk RNA-seq cohort via WGCNA-style soft-thresholded networks.
TianGzlab/OmicsClaw
Load when comparing gene expression between two conditions in bulk RNA-seq count data.
TianGzlab/OmicsClaw
Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.
TianGzlab/OmicsClaw
Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list.
TianGzlab/OmicsClaw
Load when converting gene identifiers between Ensembl, Entrez, and HGNC symbol in a bulk RNA-seq count matrix.
Categories
Load when biologically interpreting a finished verified consensus run (consensus-domains / sc-consensus-clustering) — inline DE, marker-DB lookup, and LLM cell-type naming with mandatory marker…. Consensus Interpret is an agent skill from TianGzlab/OmicsClaw. Load when biologically interpreting a finished verified consensus run (consensus-domains / sc-consensus-clustering) — inline DE, marker-DB lookup, and LLM cell-type naming with mandatory marker citations + evidence-bound next-step recommendations.
Consensus Interpret fits situations like: tasks that involve Citation management.
Run `npx skills add TianGzlab/OmicsClaw --skill consensus-interpret -a claude-code`. Or copy the skill folder (skills/spatial/consensus-interpret in TianGzlab/OmicsClaw) into .claude/skills/consensus-interpret in your project. Claude Code loads it when a task matches its description.
Run `npx skills add TianGzlab/OmicsClaw --skill consensus-interpret -a codex`. Or copy the skill folder (skills/spatial/consensus-interpret in TianGzlab/OmicsClaw) into .agents/skills/consensus-interpret 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 TianGzlab/OmicsClaw --skill consensus-interpret -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-interpret, .gemini/skills/consensus-interpret, .github/skills/consensus-interpret and .opencode/skills/consensus-interpret in your project.
Going by SKILL.md and its folder, Consensus Interpret needs Python for the scripts in its folder. Our summary lists: Python 3.
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. Review the folder before installing.
Consensus Interpret is published under the Apache-2.0 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 7.8k 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 1.3k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Consensus Interpret: Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars), Networkx (zLanqing/codex-claude-academic-skills, 4.6k stars), Citation Verification Guide (Galaxy-Dawn/claude-scholar, 5.7k stars) and Systematic Review Screener (Imbad0202/academic-research-skills, 51k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 95 skills in this directory. The repository was last updated on July 28, 2026.
Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.