Skill Claude CodeCodex
Analyze genome collinearity and syntenic blocks using MCScanX, SyRI, and JCVI for comparative genomics. Detect conserved gene order, chromosomal rearrangements, and whole-genome duplications. Use when comparing genome structure between species or identifying conserved genomic regions.
Skill Claude CodeCodex
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps, or chromosome-level visualizations.
Skill Claude CodeCodex
Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs. Use when creating circular genome visualizations.
Skill Claude CodeCodex
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes. Use when selecting colorblind-friendly palettes for figures.
Skill Claude CodeCodex
Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures. Use when creating publication figures of genomic regions with multiple data tracks.
Skill Claude CodeCodex
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 tracks.
Skill Claude CodeCodex
Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts. Use when creating static figures for papers, presentations, or reports in R.
Skill Claude CodeCodex
Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization. Use when visualizing expression patterns across samples or identifying co-expressed gene clusters.
Skill Claude CodeCodex
Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations. Use when building zoomable, hoverable plots for data exploration or web dashboards.
Skill Claude CodeCodex
Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels. Use when combining multiple plots into publication figures.
Skill Claude CodeCodex
Visualize biological networks including gene regulatory networks, protein interaction networks, and co-expression modules using NetworkX, PyVis, and Cytoscape automation. Produces interactive and publication-quality network figures. Use when creating network diagrams from interaction data, GRN results, or…
Skill Claude CodeCodex
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.
Skill Claude CodeCodex
Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot. Use when comparing overlapping gene sets, peak sets, or sample groups with more than 3 sets.
Skill Claude CodeCodex
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib. Use when visualizing differential expression or association results with gene annotations.
Skill Claude CodeCodex
Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use when performing bulk sequence downloads, handling large query results, or production-scale data retrieval.
Skill Claude CodeCodex
Run remote BLAST searches against NCBI databases using Biopython Bio.Blast. Use when identifying unknown sequences, finding homologs, or searching for sequence similarity against NCBI's nr/nt databases.
Skill Claude CodeCodex
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into Biopython objects.
Skill Claude CodeCodex
Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, or discovering database relationships.
Skill Claude CodeCodex
Search NCBI databases using Biopython Bio.Entrez. Use when finding records by keyword, building complex search queries, discovering database structure, or getting global query counts across databases.
Skill Claude CodeCodex
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.
Skill Claude CodeCodex
Query protein-protein and gene interaction databases including STRING, BioGRID, and IntAct via their REST APIs and Python clients. Retrieve interaction networks, confidence scores, and functional enrichment. Use when building protein interaction networks, contextualizing gene lists with known interactions, or…
Skill Claude CodeCodex
Run local BLAST searches using BLAST+ command-line tools. Use when running fast unlimited searches, building custom databases, performing large-scale analysis, or when NCBI servers are slow or unavailable.
Skill Claude CodeCodex
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis. Use when identifying orthologs, distant homologs, or protein family members where standard BLAST is not sensitive enough.
Skill Claude CodeCodex
Download sequencing data from NCBI SRA using the SRA toolkit. Use when downloading FASTQ files from SRA accessions, prefetching large datasets, or validating SRA downloads.