Spatial Xenium
QING1105/ezST
Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis.
Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns.
Install Sc Perturb Prep
$ npx skills add TianGzlab/OmicsClaw --skill sc-perturb-prep -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw sc-perturb-prep --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/singlecell/scrna/sc-perturb-prep .claude/skills/sc-perturb-prep && 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 "sc-perturb-prep" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-perturb-prep into .claude/skills/sc-perturb-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-perturb-prep", 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/singlecell/scrna/sc-perturb-prepType 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 sc-perturb-prep -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw sc-perturb-prep --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/singlecell/scrna/sc-perturb-prep .agents/skills/sc-perturb-prep && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "sc-perturb-prep" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-perturb-prep into .agents/skills/sc-perturb-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-perturb-prep", 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 sc-perturb-prep -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw sc-perturb-prep --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/singlecell/scrna/sc-perturb-prep .cursor/skills/sc-perturb-prep && 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 "sc-perturb-prep" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-perturb-prep into .cursor/skills/sc-perturb-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-perturb-prep", 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/singlecell/scrna/sc-perturb-prep--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 sc-perturb-prep -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw sc-perturb-prep --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/singlecell/scrna/sc-perturb-prep .gemini/skills/sc-perturb-prep && 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 "sc-perturb-prep" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-perturb-prep into .gemini/skills/sc-perturb-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-perturb-prep", 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 sc-perturb-prepInstalls 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 sc-perturb-prep -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/singlecell/scrna/sc-perturb-prep .github/skills/sc-perturb-prep && 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 "sc-perturb-prep" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-perturb-prep into .github/skills/sc-perturb-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-perturb-prep", 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 sc-perturb-prep -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 sc-perturb-prep --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/singlecell/scrna/sc-perturb-prep .opencode/skills/sc-perturb-prep && 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 "sc-perturb-prep" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-perturb-prep into .opencode/skills/sc-perturb-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-perturb-prep", 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
sc-perturb-prep- GitHub stars
- 161
- Token cost
- ~1.2k tokens
- SKILL.md length
- 435 words
- Files
- 10 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns.
- Tasks that involve Bioinformatics
- SKILL.md covers Key CLI, Workflow, Matrix Contract and Inputs & Outputs, plus 3 more sections
- Runs Python scripts from its folder; calls python
- Tasks that involve CSV and tabular files
What it does
Sc Perturb Prep is an agent skill from TianGzlab/OmicsClaw. Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns. Skip when the AnnData already has perturbation labels (use sc-perturb); raw guide-calling from FASTQ (use upstream demuxlet / cellranger guide pipelines).
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including reference files (for example `_api.py`, `examples/example_step.py` and `references/methodology.md`).
It sits in Research & Science, covering Bioinformatics and CSV and tabular files. It works with AnnData. 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.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve CSV and tabular files
Example prompts
- “/sc-perturb-prep”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit 90a3bec. 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
Sc Perturb Prep loads about 1.2k tokens when it runs, and up to ~1.7k if it reads all its reference files. Until then it costs about 89 tokens; SKILL.md has 435 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 TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 435 words, ~1,214 tokens.
Download SKILL.mdSave it as
.claude/skills/sc-perturb-prep/SKILL.md (or your agent's skills folder). This skill also uses 9 other files; get the full folder from GitHub.- name
- sc-perturb-prep
- description
- Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns. Skip when the AnnData already has perturbation labels (use sc-perturb); raw guide-calling from FASTQ (use upstream demuxlet / cellranger guide pipelines).
- tags
- singlecell, scrna, perturb-prep, perturb-seq, crispr, sgrna-assignment
sc-perturb-prep
Attach an upstream barcode-to-guide table to expression data. This is the
mapping_tsv method, not a FASTQ guide caller. It needs no pertpy installation.
Key CLI
python skills/singlecell/scrna/sc-perturb-prep/sc_perturb_prep.py --demo --output /tmp/sc_perturb_prep_demo
python skills/singlecell/scrna/sc-perturb-prep/sc_perturb_prep.py --input expression.h5ad --mapping-file mapping.tsv --output results/prepMapping columns are inferred from common names, or selected with
--barcode-column, --sgrna-column, and --target-column. Without target
values, --delimiter _ --gene-position 0 extracts the target from a guide ID.
Pass --keep-multi-guide only when retaining multi-guide cells is intended.
Workflow
Upstream: expression counts and guide calls from the same cells. Standardize
mapping columns, collapse guides per barcode, match assigned cells, retain
gene-expression features and canonicalize the matrix. Downstream: use
sc-perturb for observed perturbation signatures, or sc-preprocessing for
clustering. The API returns objects; the example step writes them explicitly.
Matrix Contract
Raw counts are preferred; canonicalization can recover counts from a layer or
raw snapshot. Inspect omicsclaw_matrix_contract and run_info for the actual
expression source. A normalized matrix is not evidence of raw counts.
Inputs & Outputs
Input: .h5ad, 10x H5 or a matrix directory, plus mapping TSV/CSV for real runs.
The CLI writes processed.h5ad, report.md, result.json,
reproducibility/commands.sh, tables/perturbation_assignments.csv,
tables/assignment_status_counts.csv, tables/perturbation_counts.csv,
tables/feature_type_summary.csv and figures/perturbation_counts.png.
tables/dropped_multi_guide_cells.csv is written only when rows were dropped.
Plot data are also written under figure_data/.
Gotchas
tables/perturbation_assignments.csvuses statusassigned,controlor retainedmulti_guide; dropped rows do not appear in the output AnnData.- Control tokens match whole words separated by punctuation:
NT_sg1is a control, whileWNT3_sg1,NTRK1_sg1andNT5E_sg1are not. Reviewtables/perturbation_assignments.csvafter choosing custom patterns. result.json→summary.n_cells_multi_guide_droppedcounts dropped multi-guide cells. No matching barcodes raisesValueErrorin the API.tables/feature_type_summary.csvdescribes the input feature types. Filtering needsvar['feature_types']; absent labels cannot identify guide or antibody features.
Show full SKILL.md (184 more words)Show less
API
<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->standardize_mapping(table, *, barcode_column=None, sgrna_column=None, target_column=None)
Return barcode, sgRNA and target_gene columns from a pandas table.
Column names may be supplied explicitly. Missing target genes are inferred later from guide names; duplicate rows and empty barcode/guide rows are removed.
collapse_assignments(mapping, *, delimiter='_', gene_position=0, control_patterns=('NT', 'NTC', 'NON-TARGET', 'NON_TARGET', 'NEGATIVE_CONTROL', 'NEG_CTRL'), control_label='NT', drop_multi_guide=True)
Return (assigned, dropped) tables with one row per barcode.
Controls match whole tokens, not substrings of gene names. Multiple guides are dropped by default; retained multi-guide cells keep their status.
attach_assignments(adata, assignments, *, pert_key='perturbation', sgrna_key='sgRNA', target_key='target_gene', species='human')
Return a gene-expression AnnData with assignments on matching cells.
The input is unchanged. Gene features and the expression matrix are canonicalized using the single-cell input contract; no pertpy is needed.
run_info(adata, *, keep: bool=True)
Return preparation provenance; keep=False removes the run record.
assignment_summary(adata)
Return assignment_status and n_cells columns for the retained cells.
perturbation_counts(adata, *, pert_key='perturbation')
Return perturbation and n_cells columns, ordered by decreasing cell count.
perturbation_counts_figure(adata, *, pert_key='perturbation', n_top=20)
Return a Figure of cell counts for up to n_top perturbations; save it separately.
<!-- api:end -->Dependencies
anndata, matplotlib, numpy, pandas, scanpy, scipy
© 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
Files
SKILL.md and 9 other files (references) in skills/singlecell/scrna/sc-perturb-prep of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- examples/example_step.py
- references/methodology.md
- references/output_contract.md
- references/parameters.md
- references/r_visualization.md
- sc_perturb_prep.py
- tests/test_prep_api.py
- tests/test_sc_perturb_prep_methods.py
Open the folder on GitHubat commit 90a3bec
Compare with similar skills
Sc Perturb Prep 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 |
|---|---|---|---|---|---|---|
| Sc Perturb Prep this skillTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Spatial XeniumQING1105/ezST | 101 | — | ~535 | Automated safety check: Pass | MIT | |
| Single2spatial Spatial MappingFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 2 repos | ~994 | Automated safety check: Pass | None | |
| Cerna Analysisaipoch/medical-research-skills | 2k | — | ~2.4k | Automated safety check: Pass | MIT | |
| Plannotate Plasmid Annotationjaechang-hits/SciAgent-Skills | 371 | 1 repos | ~4.7k | Automated safety check: Pass | GPL-3.0 | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 15 repos | ~2.8k | Automated safety check: Pass | MIT |
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Related
Works with
Categories
Questions about Sc Perturb Prep
What does Sc Perturb Prep do?
Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns. Sc Perturb Prep is an agent skill from TianGzlab/OmicsClaw. Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns.
When should I use Sc Perturb Prep?
Sc Perturb Prep fits situations like: tasks that involve Bioinformatics; tasks that involve CSV and tabular files.
How do I install Sc Perturb Prep in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill sc-perturb-prep -a claude-code`. Or copy the skill folder (skills/singlecell/scrna/sc-perturb-prep in TianGzlab/OmicsClaw) into .claude/skills/sc-perturb-prep in your project. Claude Code loads it when a task matches its description.
How do I install Sc Perturb Prep in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill sc-perturb-prep -a codex`. Or copy the skill folder (skills/singlecell/scrna/sc-perturb-prep in TianGzlab/OmicsClaw) into .agents/skills/sc-perturb-prep in your project. Codex loads it when a task matches its description.
Can I use Sc Perturb Prep 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 TianGzlab/OmicsClaw --skill sc-perturb-prep -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/sc-perturb-prep, .gemini/skills/sc-perturb-prep, .github/skills/sc-perturb-prep and .opencode/skills/sc-perturb-prep in your project.
What does Sc Perturb Prep need to run?
Going by SKILL.md and its folder, Sc Perturb Prep needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Sc Perturb Prep 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 Sc Perturb Prep 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 Sc Perturb Prep use?
Sc Perturb Prep is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Sc Perturb Prep 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. Its references folder adds about 505 tokens, read only when the agent opens those files.
What are the alternatives to Sc Perturb Prep?
Skills that share tags, products or a category with Sc Perturb Prep: Spatial Xenium (QING1105/ezST, 101 stars), Single2spatial Spatial Mapping (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Cerna Analysis (aipoch/medical-research-skills, 2k stars) and Plannotate Plasmid Annotation (jaechang-hits/SciAgent-Skills, 371 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Sc Perturb Prep?
TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 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.