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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,581 skills3 installs3,534 views
- Sc MarkersLoad when ranking cluster-level marker genes from a clustered single-cell AnnData via Scanpy Wilcoxon / t-test / logreg or COSG specificity. Skip when comparing condition-vs-control with replicates (use sc-de) or for assigning cell-type labels (use sc-cell-annotation).Votes: 0GitHub stars: 32
- Sc MetacellLoad when aggregating single cells into metacells (sample-aware coarse-grained pseudo-cells) on a normalised scRNA AnnData via SEACells or KMeans on a low-D embedding. Skip when ranking marker genes per cluster (use sc-markers) or for trajectory pseudotime ordering (use sc-pseudotime).Votes: 0GitHub stars: 32
- Sc Multi CountLoad when merging multiple single-sample scRNA-seq count matrices (one per sample-from-sc-count) into a single downstream-ready AnnData with sample labels. Skip when input is one already-merged AnnData (use sc-standardize-input) or for FASTQ→counts on each sample (use sc-count first).Votes: 0GitHub stars: 32
- Sc Pathway ScoringLoad when computing per-cell pathway / gene-set scores on a normalised scRNA AnnData via AUCell (R or Python) or Scanpy score_genes. Skip when running condition-vs-control bulk-style enrichment on top of a DE table (use sc-enrichment) or for de-novo gene-program discovery (use sc-gene-programs).Votes: 0GitHub stars: 32
- Sc Perturb PrepLoad 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 (go straight to sc-perturb) or for raw guide-calling from FASTQ (use upstream demuxlet / cellranger guide pipelines).Votes: 0GitHub stars: 32
- Sc PerturbLoad when classifying perturbed vs non-perturbed cells in a Perturb-seq / CRISPR-screen scRNA AnnData via the pertpy Mixscape workflow. Skip when guide labels are not yet attached to the expression object (run sc-perturb-prep first) or for in-silico KO predictions on unperturbed data (use sc-in-silico-perturbation).Votes: 0GitHub stars: 32
- Sc PreprocessingLoad when normalising QC'd scRNA into a PCA-ready AnnData via scanpy / Seurat / SCTransform / Pearson residuals. Skip when QC thresholds are still undecided (use sc-qc) or for batch correction across samples (use sc-batch-integration).Votes: 0GitHub stars: 32
- Sc PseudotimeLoad when ordering cells along a developmental trajectory in a normalised scRNA AnnData via DPT, Palantir, VIA, CellRank, Slingshot (R), or Monocle3 (R). Skip when ranking marker genes per cluster (use sc-markers) or for RNA velocity vector fields (use sc-velocity).Votes: 0GitHub stars: 32
- Sc QcLoad when computing per-cell QC metrics (n_genes, total counts, mt%, ribo%) on a single-cell AnnData before filtering. Skip when reads are still raw FASTQ (use sc-fastq-qc) or you want to filter cells now (use sc-filter).Votes: 0GitHub stars: 32
- Sc Standardize InputLoad when an external single-cell h5ad/h5/loom/mtx needs to be canonicalised onto the OmicsClaw AnnData contract before downstream scRNA skills run. Skip when data already came from sc-count (already canonical), or for bulk RNA-seq (use bulkrna-qc) or spatial (use spatial-preprocess).Votes: 0GitHub stars: 32
- Sc Velocity PrepLoad when generating spliced / unspliced layers from Cell Ranger BAM, FASTQ, STARsolo output, or velocyto loom — the prerequisite for sc-velocity. Skip when AnnData already has spliced+unspliced layers (go straight to sc-velocity) or for any non-velocity preprocessing (use sc-preprocessing).Votes: 0GitHub stars: 32
- Sc VelocityLoad when computing RNA velocity vectors and latent time on a scRNA AnnData with spliced / unspliced layers via scVelo (stochastic / dynamical / steady-state). Skip when input lacks spliced+unspliced layers (run sc-velocity-prep first) or for trajectory pseudotime ordering (use sc-pseudotime).Votes: 0GitHub stars: 32
- Consensus DomainsMulti-method consensus over spatial-domains. Fans out 5 methods in parallel, computes a SACCELERATOR-style base-clustering ranking, runs typed consensus (kmode / weighted / LCA), and emits a verified consensus report with the mandatory A-path banner per ADR 0010.Votes: 0GitHub stars: 32
- Consensus InterpretLLM-grounded biological interpretation of a verified typed consensus run. Reads the typed run dir + the original adata, runs inline per-cluster DE, looks up markers in a bundled tissue-keyed marker DB, and asks the chair LLM to (γ) name each cluster's likely cell type with mandatory marker citations and (β) recommend top-3 next-step skills with mandatory evidence_refs. Output banner [A+I: Interpreted on verified consensus]. Failure-mode contract per ADR 0012.Votes: 0GitHub stars: 32
- Spatial AnnotateLoad when assigning per-spot cell-type labels on a spatial AnnData via marker-gene scoring or scRNA-reference mapping (Tangram / scANVI / CellAssign). Skip when computing spot-level cell-type proportions for multi-cell-per-spot platforms (use spatial-deconv) or for tissue-domain detection (use spatial-domains).Votes: 0GitHub stars: 32
- Spatial CnvLoad when inferring copy-number variation per spot on a preprocessed spatial AnnData with chromosome-annotated genes via infercnvpy (default — log-ratio sliding-window) or Numbat (R, allele-aware clone deconvolution). Skip when `var["chromosome"]` / `var["start"]` / `var["end"]` gene-coord metadata is missing or when no normal-reference subset can be defined.Votes: 0GitHub stars: 32
- Spatial CommunicationLoad when computing ligand-receptor cell-cell communication on a preprocessed spatial AnnData with `obs[cell_type_key]` (default `leiden`) via LIANA (default), CellPhoneDB, FastCCC, or CellChat (R). Skip when running scRNA-only L-R inference (use `sc-cell-communication`) or when no cell-type labels exist (run `spatial-annotate` or `spatial-domains` first).Votes: 0GitHub stars: 32
- Spatial ConditionLoad when comparing two or more experimental conditions (treatment vs control) on a multi-sample preprocessed spatial AnnData via PyDESeq2 pseudobulk or Wilcoxon DE — needs `obs[condition_key]`, `obs[sample_key]`, and cluster labels. Skip when running per-cluster DE on one condition (use `spatial-de`) or comparing two slices without replicates.Votes: 0GitHub stars: 32
- Spatial DeLoad when ranking spatial cluster markers or comparing two spatial groups in spatial transcriptomics. Skip if the data is single-cell (use sc-de) or bulk (use bulkrna-de), or for spatially variable expression discovery (use spatial-genes).Votes: 0GitHub stars: 32
- Spatial DeconvLoad when deconvolving spot-level cell-type proportions on a Visium-style spatial AnnData using a labelled scRNA reference (FlashDeconv / Cell2location / RCTD / DestVI / Tangram / others). Skip when each spot is a single cell already (Xenium / MERFISH — use spatial-annotate) or for tissue-domain detection (use spatial-domains).Votes: 0GitHub stars: 32
- Spatial DomainsLoad when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter). Skip when ranking spatially variable genes (use spatial-genes) or for spot-level cell-type annotation (use spatial-annotate).Votes: 0GitHub stars: 32
- Spatial EnrichmentLoad when running pathway / gene-set enrichment per cluster on a preprocessed spatial AnnData via Enrichr (over-representation), GSEA (preranked), or ssGSEA (per-cell scores). Skip when ranking spatially variable genes (use `spatial-genes`) or when comparing pathways across conditions (use `spatial-condition` for DE first, then this skill on the ranked output).Votes: 0GitHub stars: 32
- Spatial GenesLoad when ranking spatially variable genes (SVGs) on a preprocessed spatial AnnData via Moran's I, SpatialDE, SPARK-X, or FlashS. Skip when detecting tissue domains (use spatial-domains) or for differential expression between groups (use spatial-de).Votes: 0GitHub stars: 32
- Spatial IntegrateLoad when removing batch effects across multiple spatial samples on a multi-batch spatial AnnData via Harmony, BBKNN, or Scanorama before downstream analysis. Skip when aligning physical slice coordinates (use spatial-register) or for single-batch data (no integration needed — go straight to spatial-domains).Votes: 0GitHub stars: 32
- Spatial Microenvironment SubsetLoad when extracting a niche / microenvironment subset around a center cell-type by spatial radius from a labelled spatial AnnData, producing a smaller AnnData of centers + their within-radius neighbours. Skip when running global tissue-domain detection (use spatial-domains) or for cross-condition comparison (use spatial-condition).Votes: 0GitHub stars: 32
- Spatial PreprocessLoad when running the foundational spatial transcriptomics QC + filtering + normalisation + HVG + PCA + neighbour-graph + Leiden pipeline on a Visium / Xenium / generic spatial AnnData. Skip when raw FASTQs need converting first (use spatial-raw-processing) or for tissue-domain detection on already-preprocessed data (use spatial-domains).Votes: 0GitHub stars: 32
- Spatial Raw ProcessingLoad when converting spatial transcriptomics raw FASTQ pairs through ST-Pipeline into a `raw_counts.h5ad` ready for spatial-preprocess. Skip when input is already a count-matrix AnnData (go straight to spatial-preprocess) or for non-spatial bulk / scRNA FASTQ (use bulkrna-read-qc / sc-fastq-qc).Votes: 0GitHub stars: 32
- Spatial RegisterLoad when aligning multiple spatial slices into a common coordinate frame on a multi-slice spatial AnnData via PASTE optimal transport or STalign image-aware registration. Skip when data is single-slice (no registration needed) or for cross-sample integration in the gene-expression space (use spatial-integrate).Votes: 0GitHub stars: 32
- Spatial StatisticsLoad when running spatial autocorrelation / hotspot / co-occurrence / neighbourhood-enrichment / Ripley K stats on a clustered spatial AnnData via squidpy. Skip when ranking spatially variable genes (use spatial-genes) or for tissue domain detection (use spatial-domains).Votes: 0GitHub stars: 32
- Spatial TrajectoryLoad when inferring pseudotime / lineage trajectories on a preprocessed spatial AnnData via DPT (default — diffusion pseudotime), CellRank (terminal-state + fate-probability), or Palantir (waypoint branch probabilities). Skip when the data has spliced/unspliced layers and you want velocity-driven dynamics (use `spatial-velocity`) or for non-spatial scRNA pseudotime (use `sc-pseudotime`).Votes: 0GitHub stars: 32
- Spatial VelocityLoad when estimating RNA velocity on a spatial AnnData with `layers["spliced"]` + `layers["unspliced"]` via scVelo (stochastic / deterministic / dynamical) or veloVI (deep generative). Skip when input lacks the spliced/unspliced layers (must be quantified upstream by velocyto / kb-python / STARsolo) or for non-spatial scRNA velocity (use `sc-velocity`).Votes: 0GitHub stars: 32
- SkillLoad when copying this directory to bootstrap a new OmicsClaw v2 skill (rename, fill in, then `git add`). Skip when an existing skill already covers the request.Votes: 0GitHub stars: 32
- Doc--> --- name: "doc" description: "Use when the task involves reading, creating, or editing `.docx` documents, especially when formatting or layout fidelity matters; prefer `python-docx` plus the bundled `scripts/render_docx.py` for visual checks." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Gh Fix Ci--> --- name: "gh-fix-ci" description: "Use when a user asks to debug or fix failing GitHub PR checks that run in GitHub Actions; use `gh` to inspect checks and logs, summarize failure context, draft a fix plan, and implement only after explicit approval. Treat external providers (for example Buildkite) as out of scope and report only the details URL." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Imagegen--> --- name: "imagegen" description: "Use when the user asks to generate or edit images via the OpenAI Image API (for example: generate image, edit/inpaint/mask, background removal or replacement, transparent background, product shots, concept art, covers, or batch variants); run the bundled CLI (`scripts/image_gen.py`) and require `OPENAI_API_KEY` for live calls." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_sh...Votes: 0GitHub stars: 32
- Openai Docs--> --- name: "openai-docs" description: "Use when the user asks how to build with OpenAI products or APIs and needs up-to-date official documentation with citations (for example: Codex, Responses API, Chat Completions, Apps SDK, Agents SDK, Realtime, model capabilities or limits); prioritize OpenAI docs MCP tools and restrict any fallback browsing to official OpenAI domains." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_fi...Votes: 0GitHub stars: 32
- Pdf--> --- name: "pdf" description: "Use when tasks involve reading, creating, or reviewing PDF files where rendering and layout matter; prefer visual checks by rendering pages (Poppler) and use Python tools such as `reportlab`, `pdfplumber`, and `pypdf` for generation and extraction." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Playwright--> --- name: "playwright" description: "Use when the task requires automating a real browser from the terminal (navigation, form filling, snapshots, screenshots, data extraction, UI-flow debugging) via `playwright-cli` or the bundled wrapper script." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Drive a real browser from the terminal using `playwright-cli`. Prefer the bundled wrapper script so t...Votes: 0GitHub stars: 32
- Screenshot--> --- name: "screenshot" description: "Use when the user explicitly asks for a desktop or system screenshot (full screen, specific app or window, or a pixel region), or when tool-specific capture capabilities are unavailable and an OS-level capture is needed." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Follow these save-location rules every time: 1) If the user specifies a path, save there. ...Votes: 0GitHub stars: 32
- Security Best Practices--> --- name: "security-best-practices" description: "Perform language and framework specific security best-practice reviews and suggest improvements. Trigger only when the user explicitly requests security best practices guidance, a security review/report, or secure-by-default coding help. Trigger only for supported languages (python, javascript/typescript, go). Do not trigger for general code review, debugging, or non-security tasks." measurable_outcome: Execute skill workflow successfully ...Votes: 0GitHub stars: 32
- Sora--> --- name: "sora" description: "Use when the user asks to generate, remix, poll, list, download, or delete Sora videos via OpenAI\u2019s video API using the bundled CLI (`scripts/sora.py`), including requests like \u201cgenerate AI video,\u201d \u201cSora,\u201d \u201cvideo remix,\u201d \u201cdownload video/thumbnail/spritesheet,\u201d and batch video generation; requires `OPENAI_API_KEY` and Sora API access." measurable_outcome: Execute skill workflow successfully with valid output within...Votes: 0GitHub stars: 32
- Speech--> --- name: "speech" description: "Use when the user asks for text-to-speech narration or voiceover, accessibility reads, audio prompts, or batch speech generation via the OpenAI Audio API; run the bundled CLI (`scripts/text_to_speech.py`) with built-in voices and require `OPENAI_API_KEY` for live calls. Custom voice creation is out of scope." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Gener...Votes: 0GitHub stars: 32
- Spreadsheet--> --- name: "spreadsheet" description: "Use when tasks involve creating, editing, analyzing, or formatting spreadsheets (`.xlsx`, `.csv`, `.tsv`) using Python (`openpyxl`, `pandas`), especially when formulas, references, and formatting need to be preserved and verified." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Transcribe--> --- name: "transcribe" description: "Transcribe audio files to text with optional diarization and known-speaker hints. Use when a user asks to transcribe speech from audio/video, extract text from recordings, or label speakers in interviews or meetings." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Transcribe audio using OpenAI, with optional speaker diarization when requested. Prefer the bu...Votes: 0GitHub stars: 32
- Canvas Design--> --- name: 'canvas-design' description: 'Create beautiful visual art in .png and .pdf documents using design philosophy. You should use this skill when the user asks to create a poster, piece of art, design, or other static piece. Create original visual designs, never copying existing artists'' work to avoid copyright violations.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- These are instruc...Votes: 0GitHub stars: 32
- Docx--> --- name: 'docx' description: '"Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction. When Claude needs to work with professional documents (.docx files) for: (1) Creating new documents, (2) Modifying or editing content, (3) Working with tracked changes, (4) Adding comments, or any other document tasks"' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. all...Votes: 0GitHub stars: 32
- Pdf--> --- name: 'pdf' description: 'Comprehensive PDF manipulation toolkit for extracting text and tables, creating new PDFs, merging/splitting documents, and handling forms. When Claude needs to fill in a PDF form or programmatically process, generate, or analyze PDF documents at scale.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Pptx--> --- name: 'pptx' description: '"Presentation creation, editing, and analysis. When Claude needs to work with presentations (.pptx files) for: (1) Creating new presentations, (2) Modifying or editing content, (3) Working with layouts, (4) Adding comments or speaker notes, or any other presentation tasks"' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Xlsx--> --- name: 'xlsx' description: '"Comprehensive spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization. When Claude needs to work with spreadsheets (.xlsx, .xlsm, .csv, .tsv, etc) for: (1) Creating new spreadsheets with formulas and formatting, (2) Reading or analyzing data, (3) Modify existing spreadsheets while preserving formulas, (4) Data analysis and visualization in spreadsheets, or (5) Recalculating formulas"' measurable_ou...Votes: 0GitHub stars: 32
- Internal Comms--> --- name: 'internal-comms' description: 'A set of resources to help me write all kinds of internal communications, using the formats that my company likes to use. Claude should use this skill whenever asked to write some sort of internal communications (status reports, leadership updates, 3P updates, company newsletters, FAQs, incident reports, project updates, etc.).' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file -...Votes: 0GitHub stars: 32