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- Alterlab Gene DbQuery NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab EnsemblQuery the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, and Variant Effect Predictor (VEP) annotations. Use when mapping gene IDs or coordinates, fetching genomic sequence, finding orthologs across species, or predicting variant consequences for genomic research. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab EnaAccess the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab ChemblQuery ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterla...Votes: 0GitHub stars: 36
- Alterlab Cdm Vfx PipelineThis skill should be used when the user asks about "VFX", "visual effects", "compositing", "green screen", "chroma key", "After Effects", "Nuke", "CGI", "motion tracking", "rotoscoping", "act as a VFX supervisor", "VFX mode", "visual effects pipeline", "matte painting", "particle effects", "3D integration", "VFX breakdown", or needs expertise in compositing workflows, visual effects planning, Nuke/After Effects pipelines, and CGI integration. Part of the AlterLab FC Skills collection (Cinema ...Votes: 0GitHub stars: 36
- Alterlab Cdm Sound DesignerThis skill should be used when the user asks about "sound design", "foley", "film sound", "sound effects", "audio post-production", "spatial audio", "sound mixing", "act as a sound designer", "sound design mode", "Dolby Atmos", "ambience design", "sound map", "music supervision", "dialogue editing", "sound for film", "surround sound", or needs expertise in sound design planning, foley workflows, music supervision, spatial audio, and mixing strategies for film. Part of the AlterLab FC Skills c...Votes: 0GitHub stars: 36
- Alterlab AnndataBuild, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterla...Votes: 0GitHub stars: 36
- Batch PipelineParallel SDLC batch runner. Analyzes a list of independent task descriptions, groups them by heuristic file-conflict prediction, dispatches one worktree-isolated background agent per task (each running the full pipeline-orchestrator: BA → Dev → QA → Sec → Docs), and aggregates results into a single batch summary. Use when: - `/sdlc:batch` invokes this skill after parsing its arguments (Step 2 of commands/batch.md) - You have 2+ independent feature/fix descriptions to run through the SDLC pip...Votes: 0GitHub stars: 35
- Oidc VersionsHow to manage and upgrade the four OIDC/OAuth third-party dependencies used by OwlMeans OIDC packages. Covers exact-pin policy, official doc anchors, breaking-change checklists for each lib, the OwlMeans isolation principle, and the verification flow across common and downstream repos. Auto-invoked when touching oidc-provider, openid-client, jose, or oidc-client-ts version strings in package.json files.Votes: 0GitHub stars: 3
- Owlmeans ContextHow to use @owlmeans/context — the context every OwlMeans app looks things up on, context.service() and resource lookups, typed entrypoint protocol references, and entitySlug vs entityId addressing. Auto-invoked when importing from @owlmeans/context or obtaining a service, resource or entrypoint from a context.Votes: 0GitHub stars: 3
- Shadcn VersionsHow to update versions of shadcn UI primitives, Tailwind CSS v4, and related UI libs across all shadcn-based OwlMeans web packages. Distinct from the @owlmeans/* package version sync (see [[versions]] skill). Use when bumping tailwind, shadcn components, or utility libs.Votes: 0GitHub stars: 3
- Shadcn VersionsHow to update versions of shadcn UI primitives, Tailwind CSS v4, and related UI libs across all shadcn-based OwlMeans web packages. Distinct from the @owlmeans/* package version sync (see [[versions]] skill). Use when bumping tailwind, shadcn components, or utility libs.Votes: 0GitHub stars: 3
- PublishingHow to cut a release of the OwlMeans Common monorepo — detect which packages really changed against the registry, bump only those plus their dependents, and publish exactly that set under the right dist-tag. Use when releasing, bumping versions, or publishing any @owlmeans/* package.Votes: 0GitHub stars: 3
- Owlmeans ContextHow to use @owlmeans/context — the context every OwlMeans app looks things up on, context.service() and resource lookups, typed entrypoint protocol references, and entitySlug vs entityId addressing. Auto-invoked when importing from @owlmeans/context or obtaining a service, resource or entrypoint from a context.Votes: 0GitHub stars: 3
- Oidc VersionsHow to manage and upgrade the four OIDC/OAuth third-party dependencies used by OwlMeans OIDC packages. Covers exact-pin policy, official doc anchors, breaking-change checklists for each lib, the OwlMeans isolation principle, and the verification flow across common and downstream repos. Auto-invoked when touching oidc-provider, openid-client, jose, or oidc-client-ts version strings in package.json files.Votes: 0GitHub stars: 3
- Wheatomics QueryWheatOmics 平台（wheatomics.sdau.edu.cn）数据查询技能。当用户需要查询小麦/麦族基因信息、表达谱、共表达、蛋白互作、同源与共线性、序列获取、BLAST、GO/KEGG 富集、变异数据、文献检索或引物设计时使用。Votes: 0GitHub stars: 3
- Ncbi Reference To ClusterSelect, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.Votes: 0GitHub stars: 3
- Scrnaseq PipelineEnd-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.Votes: 0GitHub stars: 3
- Clinical InterpretationClinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.Votes: 0GitHub stars: 3
- Spatial DomainsIdentify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots considering both expression and spatial context to define anatomical regions. Use when identifying tissue domains or spatial regions.Votes: 0GitHub stars: 3
- Hisat2 AlignmentAlign RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.Votes: 0GitHub stars: 3
- Tree IoRead, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees.Votes: 0GitHub stars: 3
- Similarity NetworkSimilarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity networks.Votes: 0GitHub stars: 3
- Taxonomy AssignmentTaxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.Votes: 0GitHub stars: 3