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- Scvi ToolsDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.Votes: 0GitHub stars: 4
- ScanpyStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.Votes: 0GitHub stars: 4
- PysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.Votes: 0GitHub stars: 4
- PydicomPython library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, ...Votes: 0GitHub stars: 4
- Molecular CloningMolecular cloning simulation and design. PCR amplicon prediction, restriction enzyme digestion, Golden Gate and Gibson assembly simulation, primer design, CRISPR sgRNA design, and plasmid annotation. For protein-level sequence analysis use biopython or esm; for database lookups use gene-database or ensembl-database.Votes: 0GitHub stars: 4
- EtetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.Votes: 0GitHub stars: 4
- BioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.Votes: 0GitHub stars: 4
- Bio Copy Number Germline Cnv InterpretationClassify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV and AnnotSV for semi-automated scoring. Covers the separate copy-number-loss and copy-number-gain rubrics, the five-tier classification, ClinGen haploinsufficiency/triplosensitivity and dosage-sensitive regions, de novo and segregation evidence, and population-frequency benign evidence. Use when assigning pathogenic/likely-path...Votes: 0GitHub stars: 4
- Bio Comparative Genomics Gene Tree Species Tree ReconciliationReconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content sign...Votes: 0GitHub stars: 4
- Bio Comparative Genomics Ancestral ReconstructionReconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs...Votes: 0GitHub stars: 4
- Bio Long Read SplicingAnalyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMAT...Votes: 0GitHub stars: 4
- Biological KnowledgeBiological knowledge: query curated assertions and reference databases for genes, variants, pathways, regulation, cell types, reference atlases, perturbation-derived relationships, phenotypes, therapeutic targets, drugs, interactions, annotations, signatures, compounds, and predicted structures. Use for identifiers, marker sets, gene sets, associations, ontologies, database facts, and cross-database coverage.Votes: 0GitHub stars: 4
- Parallax Thematic ScreenThematic stock screen and idea analysis: build a stock universe from a theme, score top picks, layer optional macro context and regime signals, compare peers, and check financials via Parallax MCP tools. Triggers: 'screen for [theme]', 'trade ideas around X', 'thematic ideas for Y', 'stocks in Z theme', 'new ideas in [sector]'. NOT for single stock analysis (use /parallax-should-i-buy), not for portfolio review (use /parallax-client-review), not for a country or region screen (use /parallax-c...Votes: 0GitHub stars: 5
- Parallax Stress House ViewStress-test the active CIO house view against fresh Parallax macro data and internal consistency. Emits a per-run report and a hash-chained audit entry. Optionally hands off to /parallax-load-house-view --edit to incorporate updates. NOT for portfolio construction (use /parallax-portfolio-builder), not for one-off scenario reactions (use /parallax-scenario-analysis).Votes: 0GitHub stars: 5
- Parallax Thematic ScreenThematic stock screen and idea analysis: build a stock universe from a theme, score top picks, layer optional macro context and regime signals, compare peers, and check financials via Parallax MCP tools. Triggers: 'screen for [theme]', 'trade ideas around X', 'thematic ideas for Y', 'stocks in Z theme', 'new ideas in [sector]'. NOT for single stock analysis (use /parallax-should-i-buy), not for portfolio review (use /parallax-client-review), not for a country or region screen (use /parallax-c...Votes: 0GitHub stars: 5
- Nft StandardsImplement NFT standards (ERC-721, ERC-1155) with proper metadata handling, minting strategies, and marketplace integration. Use when creating NFT contracts, building NFT marketplaces, or implementi...Votes: 0GitHub stars: 36
- Wiki Page WriterGenerates rich technical documentation pages with dark-mode Mermaid diagrams, source code citations, and first-principles depth. Use when writing documentation, generating wiki pages, creating tech...Votes: 0GitHub stars: 36
- Skill CreatorThis skill should be used when the user asks to create a new skill, build a skill, make a custom skill, develop a CLI skill, or wants to extend the CLI with new capabilities. Automates the entire s...Votes: 0GitHub stars: 36
- Mcp BuilderGuide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate exte...Votes: 0GitHub stars: 36
- Obsidian Clipper Template CreatorGuide for creating templates for the Obsidian Web Clipper. Use when you want to create a new clipping template, understand available variables, or format clipped content.Votes: 0GitHub stars: 36
- RfdiffusionGenerate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold2-...Votes: 0GitHub stars: 26
- To IssuesBreak a plan, spec, or PRD into independently-grabbable issues on the project issue tracker using tracer-bullet vertical slices. Use when user wants to convert a plan into issues, create implementation tickets, or break down work into issues.Votes: 0GitHub stars: 3
- Stalled Agent RecoveryRecover gracefully when an Agent tool dispatch stalls, times out, or returns mid-edit. Detect via duration > 300s + partial-edit signature, locate agent's last write target, complete inline. Use when an Agent invocation returns a non-completion message, when the agent's last sentence is mid-thought, or when you suspect token budget hit.Votes: 0GitHub stars: 3
- Schema Markup GuideGenerates schema markup recommendations with JSON-LD code for articles, products, FAQs, and local businesses. Use when adding structured data to your website.Votes: 0GitHub stars: 3