The library

pipeline-chipseq · Processing ChIP-seq data with treatment/control comparisons and IDR replicate analysis.

configuring-tauri-apps · Fine-tuning Tauri desktop app security, permissions, and platform behavior.

matplotlib · Creating publication-quality scientific plots with full customization control.

pipeline-cutandrun · Processing CUT&RUN epigenomic data with targeted chromatin profiling.

configuring-tauri-capabilities · Fine-tuning Tauri desktop app security, permissions, and platform behavior.

medchem · Designing drug molecules with integrated ADME and toxicity assessment.

eve-lab-topology-validation · Validating enzymatic reaction networks for synthetic biology feasibility.

configuring-tauri-csp · Fine-tuning Tauri desktop app security, permissions, and platform behavior.

modal · Running Python functions serverless with GPU/TPU for batch compute.

pipeline-guide · Selecting and executing appropriate pipeline for your genomics workflow.

configuring-tauri-http-headers · Fine-tuning Tauri desktop app security, permissions, and platform behavior.

molecular-dynamics · Running classical MD simulations with analysis pipelines and GPU acceleration.

pipeline-hic · Processing Hi-C FASTQ to 3D contact matrices and loop calls.

nx-plugins · Extending NestJS monorepo with custom plugins and integrations.

configuring-tauri-permissions · Fine-tuning Tauri desktop app security, permissions, and platform behavior.

molfeat · Quickly featurizing chemical structures for QSAR, virtual screening, or deep learning without manual descriptor engineering.

pipeline-rnaseq · Processing bulk RNA-seq from raw data to publication-ready expression matrices following ENCODE standards.

flags · Quickly debugging why a feature behaves differently across canary/next/experimental channels.

configuring-tauri-scopes · Restricting desktop app file access to safe directories without implementing custom auth per command.

networkx · Analyzing organizational hierarchies, social networks, or biological interaction networks without custom graph code.

pipeline-wgbs · Generating publication-ready methylation maps from whole-genome bisulfite sequencing following ENCODE methylation standards.

spk-admin-dashboard · Quickly finding the dashboard URL without manually hunting for localhost ports or PIDs.

connect-apps · Automating one-off integrations with external services (Gmail, Slack, GitHub) without building custom auth.

neurokit2 · Rapidly extracting heart rate, HRV, brainwave power, or autonomic indices from raw biosignals without implementing DSP.

publication-trust · Deciding whether to build downstream analysis on a paper's methods before wasting resources on unreliable findings.

connect · Orchestrating multi-app workflows (send alert → create issue → post to Slack) without hardcoding integrations.

neuropixels-analysis · Processing Neuropixels recordings to high-quality sorted units without manual curation optimization.

quality-assessment · Quickly deciding if a sequencing sample meets publication standards without manual QC checklist.

stage · Bundling code changes without manually juggling staging, commits, and conflict resolution.

connections-optimizer · Reducing inter-service latency without manual network tuning or load-balancer rule writing.

regulatory-elements · Linking noncoding variants or peaks to biological function without training custom classification models.

content-engine · Quickly repurposing one article into tweets, LinkedIn posts, and emails without rewriting each variant.

omero-integration · Centralizing large imaging datasets with rich metadata without custom database schema design.

scientific-writing · Rapidly drafting a paper outline before filling in analyses, rather than starting from a blank page.

twmd · Previewing tweet formatting before posting without trial-and-error on the platform.

open-notebook · Research teams needing self-hosted document analysis with data privacy and multi-speaker podcast generation.

scrna-meta-analysis · Building cell atlases and assessing reproducibility of single-cell findings across studies with detection-aware quality filtering.

speckit-tasks · Spec Kit workflow Phase 4 (tasks generation) when translating designs into implementation dependencies.

opentrons-integration · Production liquid-handling workflows requiring full Protocol API v2 access and hardware-specific module control.

search-encode · Discovering existing ENCODE experiments before downloading when exploring what data is available for a tissue/assay.

refactor · Large refactoring efforts where test coverage provides a safety net to avoid breaking changes.

context-window-management · Multi-turn conversations where context is overflowing, improving model behavior when fed too much historical data.

commit · Automated commit creation when changes are ready and only a summary message is needed.

continuous-agent-loop · Autonomous agent systems that need reliable iteration with quality controls and safe recovery from failures.

pacsomatic · Reproducible tumor-normal variant calling when validation and artifact generation must precede execution.

single-cell-encode · Building or validating cell type annotations when authoritative single-cell reference data exists in ENCODE.

continuous-learning-v2 · Long-running development projects where patterns repeat across sessions and can be learned and reused.

paper-lookup · Quick literature discovery and retrieval when you know the title, DOI, or author and need the full paper.

track-experiments · Research projects with many runs where reproducibility and parameter comparison are critical.

conversation-memory · Multi-session projects where maintaining continuity and avoiding re-explanation is valuable.