Explorar skills

protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing. Public access free; auth needed for private or publishing. Pair with opentrons-protocol-api or benchling-integration to execute.

Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons OT-2, or a simulator without vendor lock-in. For protocol automation, method dev, plate reformatting, serial dilutions, and Python lab workflows.

Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with uncertainty. Unified setup→train→extract API on AnnData. Use harmony-batch-correction for fast linear correction without deep learning; muon for multi-modal MuData workflows.

Execute the MAD-based single-cell RNA-seq QC workflow (scripts + Python API) to filter low-quality cells and emit reports plus filtered AnnData files.

Orchestrate multi-simulation campaigns including parameter sweeps, batch jobs, and result aggregation. Use for running parameter studies, managing simulation batches, tracking job status, combining results from multiple runs, or automating simulation workflows.

Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.

Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl VEP for REST API; SnpEff for fast CLI with pre-built genomes.

Unified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan, Maxwell, Blackrock), preprocess, run 10+ sorters (Kilosort4, SpykingCircus2, Tridesclous, MountainSort5) via one API, compute quality metrics (SNR, ISI, firing rate), compare sorters, export NWB/Phy. For format-agnostic multi-sorter workflows. For Neuropixels-specific PSTH/decoding use

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.

X/Twitter API integration for posting tweets, threads, reading timelines, search, and analytics. Covers OAuth auth patterns, rate limits, and platform-native content posting. Use when the user wants to interact with X programmatically.

Parallel BMAD workflow orchestration using git worktrees and tmux. USE WHEN BMAD parallel, orchestrate sprint, run stories in parallel, worktree orchestration, sprint acceleration, parallel dev stories, bmad worktree, parallelize BMAD, accelerate epic.

Git worktree management with tmux and iTerm2 integration. Use when creating isolated dev environments, managing parallel feature branches, switching contexts without stashing, or running multiple Claude instances. Covers worktree creation, tmux window management, iTerm2 tabs, and cleanup workflows.