scientific-computing
0
design-dsrna
Design dsRNA candidates using sliding window algorithm
katalyzeAI
research
sorting
stars
current ordering strategy
query
all entries
refine the visible subset
bioinformatics
0
integrate-road-network
Integrate real-world street networks into VRP problems using OpenStreetMap data. Use when loading real map data, creating instances from actual locations, computing network-based distances, or building tutorials with real-world scenarios. Guides through installation, loading areas, extracting nodes, computing distance matrices, and creating PDPTW instances from map data.
dudusoar
research
scientific-computing
0
bio-igv
This skill should be used when the user needs to visualize BAM alignment files in IGV (Integrative Genomics Viewer). Triggers include requests to generate IGV screenshots, visualize genomic regions with multiple BAM tracks, or create batch visualizations for WGS analysis results.
dakesan
research
bioinformatics
0
sparse-expression-visualization
Visualization patterns for sparse single-cell gene expression data. Trigger: boxplots flat at zero, single-cell expression plots, sparse data visualization
smith6jt-cop
research
scientific-computing
0
envi-pkg-local-improved
ENVI spatial transcriptomics analysis toolkit - comprehensive documentation with tutorials and Python source code
Ketomihine
research
bioinformatics
0
archr-local
ArchR docs served from downloaded_docs/archr_scrape - comprehensive scATAC-seq analysis toolkit with all HTML files explicitly listed
Ketomihine
research
bioinformatics
0
network-meta-analysis
Network meta-analysis for comparing multiple treatments
matheus-rech
research
scientific-computing
0
ligandmpnn-reference
LigandMPNN sequence design reference. Use when working with LigandMPNN, ProteinMPNN, sequence design, amino acid biasing, fixed residues, temperature, side chain packing, or membrane protein design.
polaires
research
scientific-computing
0
alphafold-database
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
Sologa
research
bioinformatics
0
mip-research
Phase 1 of MIP pipeline - Research Gatsby metaphor scholarship, establish seed CMT systems, and document MIP procedure for annotators.
gjohnsx
research
bioinformatics
0
trial-sequential-analysis
Teach Trial Sequential Analysis (TSA) for controlling type I and II errors in cumulative meta-analyses. Use when users need to assess if meta-analysis has sufficient information, want to avoid premature conclusions, or need to plan future trials.
matheus-rech
research
bioinformatics
0
segmentation
Isolates skin regions from background clutter using calibrated thresholds for downstream analysis
do-ops885
research
bioinformatics
0
context-map
Fast repository indexing for RLM workflows. Use before analysis to reduce context drift.
oornnery
research
scientific-computing
0
lammps-simulation
Run LAMMPS molecular dynamics simulations. Use when asked to run MD simulations, energy minimization, equilibration, production runs, or calculate properties like diffusion, RDF, MSD. Supports both CPU and GPU execution.
fl-sean03
research
bioinformatics
0
curate-bulk-rnaseq
Process bulk RNA-seq datasets for VEuPathDB resources
VEuPathDB
research
scientific-computing
0
bio-cosmic
This skill should be used when the user needs to query COSMIC Cancer Gene Census to check if genes are known cancer genes. Triggers include requests to annotate genes with cancer information, check if variants are in cancer genes, or retrieve cancer gene properties from COSMIC database.
dakesan
research
bioinformatics
0
ml-integration-patterns
Machine learning integration patterns for rRNA-Phylo covering three use cases - rRNA sequence classification (supervised learning with sklearn/PyTorch), multi-tree consensus (ensemble methods), and generative tree synthesis (GNNs/transformers). Includes feature engineering, model training, hyperparameter tuning, model serving, versioning, and evaluation metrics for bioinformatics ML workflows.
roeimed0
research
bioinformatics
0
seurat-single-cell-analysis
R-based single cell analysis using Seurat v5 for .rds/.rdata files
Ketomihine
research
bioinformatics
0
time-to-event-methods
Survival analysis methods including weighted logrank, MaxCombo, RMST, and milestone tests. Use when analyzing TTE data or choosing analysis methods for non-proportional hazards.
choxos
research
bioinformatics
0
meta-analysis
Complete meta-analysis generation for neurosurgical outcomes
matheus-rech
research
scientific-computing
0
tidy-itc-workflow
Master tidy modelling patterns for ITC analyses following TMwR principles. Covers workflow structure, consistent interfaces, reproducibility best practices, and data validation. Use when setting up ITC analysis projects or building pipelines.
choxos
research