Comments
Code comments and annotations
etetoolkit
by jaechang-hits
"ETE Toolkit (ETE3) is a Python environment for phylogenetic tree analysis, manipulation, and visualization. Parse Newick/NHX/PhyloXML trees, traverse and annotate nodes, render publication-quality figures with TreeStyle/NodeStyle, integrate NCBI taxonomy for taxon-aware operations, and run PhyloTree workflows for comparative genomics. Use for building species trees, gene family evolution analysis, and annotated tree figures."
bioservices-multi-database
by jaechang-hits
Unified Python interface to 40+ bioinformatics web services via bioservices library. Query UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem compounds, run BLAST searches, map identifiers across databases, retrieve GO annotations, and find protein-protein interactions. For single-database deep queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database integration workflows.
my-skill-name
by dadbodgeoff
Brief description of what this skill does and when to use it. Be specific about capabilities and use cases to help agents decide when to load this skill.
bcftools-variant-manipulation
by jaechang-hits
"Command-line toolkit for VCF/BCF variant file manipulation. Filter, merge, annotate, query, normalize, and compute statistics on variant call files. Essential for post-variant-calling pipelines: quality filtering, multi-sample merging, rsID annotation, and genotype extraction. Companion to samtools in the HTSlib ecosystem. Use GATK instead for complex indel realignment during variant calling; use VCFtools instead for population genetics statistics."
clinpgx-database
by jaechang-hits
"Query PharmGKB (Clinical Pharmacogenomics) database via REST API for drug-gene interactions, clinical annotations, dosing guidelines (CPIC, DPWG), variant-drug associations, and pharmacogenomic pathways. Search by gene, drug, rsID, or pathway. No authentication required. For somatic cancer pharmacogenomics use cosmic-database or opentargets-database; for drug structures use chembl-database-bioactivity."
napari-image-viewer
by jaechang-hits
"Interactive multi-dimensional image viewer for scientific microscopy data. Napari displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, and Tracks layers; supports real-time annotation, plugin-based analysis, and headless screenshot export. Core visualization tool for bioimage analysis workflows. Use ImageJ/FIJI for macro-based processing; use napari for Python-native interactive visualization and plugin-based deep learning segmentation review."
agent-team-orchestration
by LeoYeAI
"Orchestrate multi-agent teams with defined roles, task lifecycles, handoff protocols, and review workflows. Use when: (1) Setting up a team of 2+ agents with different specializations, (2) Defining task routing and lifecycle (inbox → spec → build → review → done), (3) Creating handoff protocols between agents, (4) Establishing review and quality gates, (5) Managing async communication and artifact sharing between agents."
add-educational-comments
by LeoYeAI
'Add educational comments to the file specified, or prompt asking for file to comment if one is not provided.'
gene-database
by jaechang-hits
"Query NCBI Gene via E-utilities for curated gene records across 1M+ taxa. Retrieve official gene symbols, aliases, RefSeq accessions, summary descriptions, genomic coordinates, GO annotations, and interaction data. Use for gene ID resolution, cross-species queries, and gene function summaries. For sequence retrieval use Ensembl; for expression data use geo-database."
omero-integration
by jaechang-hits
"OMERO is an open-source platform for biological image data management. Use the omero-py Python client to connect to an OMERO server, search and retrieve images as numpy arrays, annotate images with tags and key-value pairs, manage ROIs, and integrate OMERO image data into downstream analysis pipelines — all programmatically without the OMERO desktop GUI."
encode-database
by jaechang-hits
"Query the ENCODE Portal REST API for regulatory genomics data: TF ChIP-seq experiments, ATAC-seq/DNase-seq accessibility peaks, histone mark tracks, and RNA-seq datasets across 1000+ cell types and tissues. Search experiments by assay, biosample, or target protein; download BED/bigWig files; retrieve candidate cis-regulatory elements (cCREs) from ENCODE SCREEN by genomic region or gene. Use for finding regulatory tracks to annotate variants, identifying open chromatin in a cell type of interest, and downloading peak files for ChIP-seq or ATAC-seq analysis. For regulatory variant scoring use regulomedb-database; for GWAS associations use gwas-database."
cosmic-database
by jaechang-hits
"Query COSMIC (Catalogue Of Somatic Mutations In Cancer) for cancer somatic mutations, gene census data, mutational signatures, drug resistance variants, and cancer gene annotations. REST API v3.1 supports gene/sample/variant queries. Free registration required. For germline clinical variants use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity."
featurecounts-rna-counting
by jaechang-hits
"Counts aligned RNA-seq reads overlapping gene features in a GTF annotation. Takes sorted BAM files from STAR alignment and a GTF file; outputs a tab-delimited count matrix per gene across all samples. Handles strandedness (0=unstranded, 1=stranded, 2=reverse-stranded), paired-end, and multi-sample batch counting in a single command. Use Salmon instead for alignment-free quantification; use featureCounts when STAR BAMs already exist and a gene-level count matrix is needed."
bedtools-genomic-intervals
by jaechang-hits
"Toolkit for genomic interval operations on BED, BAM, GFF, VCF files. Find overlapping regions, merge adjacent intervals, calculate coverage depth, extract FASTA sequences, find nearest features, and manipulate interval coordinates. Essential for ChIP-seq peak annotation, target region filtering, and genome arithmetic. Use tabix instead for indexed single-region queries; use deeptools for normalized bigWig coverage."
nnunet-segmentation
by jaechang-hits
"Train and deploy automated medical image segmentation models using nnU-Net's self-configuring framework that auto-selects optimal architecture, preprocessing, and training for any modality. Supports CT, MRI, microscopy, and ultrasound with 2D, 3D full-res, 3D low-res, and cascade configurations. Pipeline: convert dataset → plan and preprocess → train (5-fold cross-validation) → find best configuration → predict → ensemble. Use when classical segmentation fails and annotated training data is available."
ena-database
by jaechang-hits
"European Nucleotide Archive (ENA) REST API access for genomic sequences, raw reads, assemblies, and annotations. Portal API search with query syntax, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM download URLs, taxonomy queries, cross-references. For multi-database Python queries prefer bioservices; for NCBI-specific queries use pubmed-database or Biopython Entrez."
celltypist-cell-annotation
by jaechang-hits
"Automated cell type annotation for scRNA-seq data using pre-trained logistic regression models. CellTypist ships 45+ models covering immune cells, gut, lung, brain, fetal tissues, and cancer microenvironments. Inputs a normalized AnnData; outputs per-cell predicted labels, majority-vote cluster labels, and confidence scores. Use when you want fast, reproducible, reference-model-backed annotation without manual marker inspection."
ensembl-database
by jaechang-hits
"Query Ensembl REST API for gene/transcript/variant annotations across 300+ species. Retrieve gene info by symbol/ID, sequence, cross-references (HGNC, RefSeq, UniProt), variants, regulatory features, comparative genomics. For bulk local access use pyensembl; for pathway lookups use kegg-database or reactome-database."
data-visualization
by inference-sh
"Data visualization with chart selection, color theory, and annotation best practices. Covers chart types (bar, line, scatter, heatmap), axes rules, and storytelling with data. Use for: charts, graphs, dashboards, reports, presentations, infographics, data stories. Triggers: data visualization, chart, graph, data chart, bar chart, line chart, scatter plot, data viz, visualization, dashboard chart, infographic data, data presentation, chart design, plot, heatmap, pie chart alternative"
linkedin-content
by inference-sh
"LinkedIn post writing with hook formulas, formatting rules, and engagement patterns. Covers post types, algorithm signals, character limits, and content pillars. Use for: LinkedIn posts, professional content, thought leadership, B2B content, personal branding. Triggers: linkedin post, linkedin content, linkedin writing, linkedin strategy, linkedin engagement, linkedin algorithm, linkedin hook, linkedin formatting, thought leadership, professional content, b2b content, linkedin growth"
data-visualization
by inference-sh
"Data visualization with chart selection, color theory, and annotation best practices. Covers chart types (bar, line, scatter, heatmap), axes rules, and storytelling with data. Use for: charts, graphs, dashboards, reports, presentations, infographics, data stories. Triggers: data visualization, chart, graph, data chart, bar chart, line chart, scatter plot, data viz, visualization, dashboard chart, infographic data, data presentation, chart design, plot, heatmap, pie chart alternative"
product-hunt-launch
by inference-sh
"Product Hunt launch optimization with specific specs, timing, and gallery strategy. Covers taglines, gallery images, maker comments, and launch day tactics. Use for: product launches, startup launches, side project launches, Product Hunt optimization. Triggers: product hunt, ph launch, product hunt launch, launch strategy, product launch, startup launch, product hunt tips, product hunt gallery, ph optimization, launch day, product hunt maker"
jspecify-nullness
by alexandru
JSpecify nullness annotations for Java APIs and tooling. Use when adopting or migrating JSpecify annotations, designing null-safe Java signatures and generics, or interpreting tool conformance and Kotlin interop.
pr-apply-review
by ryoppippi
Fetch and apply review comments from the current PR. Use when you need to address PR feedback.