GitHub
bio-restriction-fragment-analysis
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests.
☆ 299View skill
databases bioinformatics AI Skills
Discover databases bioinformatics skills, compare source repositories and read the instructions for each workflow.
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bio-metagenomics-strain-tracking
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, tra...
☆ 299View skill
GitHub
bio-chipseq-differential-binding
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values.
☆ 299View skill
GitHub
bio-workflows-proteomics-pipeline
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma.
☆ 299View skill
GitHub
bio-pdb-structure-navigation
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use for accessing models, chains, residues, and atoms, iterating over structure levels, extracting sequences, identifying residue types,...
☆ 299View skill
GitHub
bio-data-visualization-genome-tracks
Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV. Use when visualizing genomic data at specific loci with multiple aligned tra...
☆ 299View skill
GitHub
bio-chipseq-visualization
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions.
☆ 299View skill
GitHub
bio-read-alignment-star-alignment
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Use for RNA-seq data requiring splice-aware alignment. Supports two-pass mode for novel splice junction discovery.
☆ 299View skill
GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 283View skill
GitHub
nextflow-development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core,...
☆ 210View skill
GitHub
single-cell-rna-qc
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering lo...
☆ 210View skill
GitHub
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS sys...
☆ 210View skill
GitHub
scvi-tools
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq mul...
☆ 210View 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...
☆ 191View skill
GitHub
claude-scientific-skills
Comprehensive collection of 128+ ready-to-use scientific skills for Claude enabling research across biology, chemistry, medicine, genomics, and advanced analysis domains.
☆ 129View skill
GitHub
fiftyone-embeddings-visualization
Visualize datasets in 2D using embeddings with UMAP or t-SNE dimensionality reduction. Use when users want to explore dataset structure, find clusters in images, identify outliers, color samples by class or met...
☆ 124View skill
GitHub
fiftyone-find-duplicates
Find duplicate or near-duplicate images in FiftyOne datasets using brain similarity computation. Use when users want to deduplicate datasets, find similar images, cluster visually similar content, or remove red...
☆ 124View 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...
☆ 124View skill
GitHub
reasoning-inductive
Extract patterns and generalizations from multiple observations. Use when detecting recurring themes, building predictive rules, or identifying systemic behaviors from accumulated data. Produces validated patte...
☆ 123View skill
GitHub
busco-phylogeny
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation
☆ 123View skill
GitHub
project-research
Research workflow patterns specific to {project}. Covers research agent coordination, source management, and synthesis strategies.
☆ 122View skill
GitHub
lifecycle
Guidance for managing R package lifecycle according to tidyverse principles using the lifecycle package. Use when: (1) Setting up lifecycle infrastructure in a package, (2) Deprecating functions or arguments, (...
☆ 94View skill
GitHub
chai
Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-lig...
☆ 91View skill
GitHub
pdb
Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific...
☆ 91View skill
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