GitHub
gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment...
☆ 9View skill
databases bioinformatics AI Skills
Discover databases bioinformatics skills, compare source repositories and read the instructions for each workflow.
Categories: databases bioinformatics
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GitHub
arboreto
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcripti...
☆ 9View skill
GitHub
networkx
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing gra...
☆ 9View skill
GitHub
pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal pro...
☆ 9View skill
GitHub
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spa...
☆ 9View skill
GitHub
understand
Multi-specialist collaborative analysis to understand how features, functions, or components work
☆ 9View skill
GitHub
biomni
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical rese...
☆ 9View skill
GitHub
busco-phylogeny
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation
☆ 8View skill
GitHub
biogeobears
Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Use when users request biogeographic reconstruction, ancestral range estimation, or want to analyze species distributions on phylog...
☆ 8View skill
GitHub
running-clustering-algorithms
Execute clustering algorithms (K-means, DBSCAN, hierarchical) to identify data groups. Use when requesting "run clustering", "cluster analysis", or "group data points".
☆ 7View skill
GitHub
engineering-features-for-machine-learning
Create, select, and transform features to improve machine learning model performance. Handles feature scaling, encoding, and importance analysis. Use when asked to "engineer features" or "select features".
☆ 7View skill
GitHub
berdl
Query the KBase BERDL (BER Data Lakehouse) pangenome database. Use when the user asks to explore pangenome data, query species information, get genome statistics, analyze gene clusters, or access functional ann...
☆ 7View skill
GitHub
orcawave-aqwa-benchmark
Cross-validation specialist for comparing OrcaWave and AQWA diffraction analysis results. Provides statistical comparison, peak value validation, and automated benchmark reporting for hydrodynamic coefficient v...
☆ 6View skill
GitHub
orcaflex-visualization
Generate visualizations from OrcaFlex simulations including model views, time series plots, range graphs, and interactive HTML reports using Plotly for comprehensive analysis presentation.
☆ 6View skill
GitHub
orcaflex-file-conversion
Convert OrcaFlex files between formats (.dat, .yml, .sim) for digital analysis and automation. Supports bidirectional conversion, batch processing, and format standardization.
☆ 6View skill
GitHub
shader-sdf
Signed Distance Functions (SDFs) in GLSL—2D/3D shape primitives, boolean operations (union, intersection, subtraction), smooth blending, repetition, and raymarching fundamentals. Use when creating procedural sh...
☆ 6View skill
GitHub
biology-comprehensive-guide
Comprehensive biology expert from molecular biology to ecology, covering cell biology, genetics, evolution, and physiology
☆ 6View skill
GitHub
nixtla-anomaly-detector
Detects anomalies in time series data using TimeGPT. Identifies outliers, level shifts, and trend breaks without model training. Use when identifying anomalies, outliers, or unusual patterns in time series. Tri...
☆ 6View skill
GitHub
nixtla-research-assistant
Research and summarize Nixtla ecosystem updates and time-series forecasting content from the web and GitHub. Use when gathering release notes, recent changes, or best-practice references. Trigger with "Nixtla u...
☆ 6View skill
GitHub
causal-tracing
Causal mediation analysis to identify which model components mediate specific behaviors. Use when investigating how information flows through the network and which neurons or layers are causally responsible for...
☆ 6View skill
GitHub
td-hierarchical-clustering
Hierarchical clustering for nested data grouping
☆ 6View skill
GitHub
td-npath
Path analysis for sequential event patterns
☆ 6View skill
GitHub
td-pacf
Partial auto-correlation analysis for direct lag relationships
☆ 6View skill
GitHub
td-change-point
Change point detection in time series for structural breaks
☆ 6View skill
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