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14810 skills availablebio-workflows-scrnaseq-pipeline
Complete workflow from 10X Genomics Cell Ranger output to annotated cell types. 10X data (filteredfeaturebcmatrix) [1. L...
pdx-model-analysis-agent
The PDX Model Analysis Agent provides AI-driven analysis of patient-derived xenograft models for preclinical drug testin...
bio-chipseq-differential-binding
Reference examples tested with: DESeq2 1.42+, edgeR 4.0+ Before using code patterns, verify installed versions match. If...
ontology-explorer
Enable an agent to understand, navigate, and query the structure of materials science ontologies without loading verbose...
alphafold
| Requirement | Minimum | Recommended | |-------------|---------|-------------| | Python | 3.8+ | 3.10 | | CUDA | 11.0+ ...
bio-batch-processing
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions...
bio-rna-quantification-featurecounts-counting
Count reads mapping to genomic features (genes, exons) from BAM files. featureCounts -a annotation.gtf -o counts.txt ali...
bio-data-visualization-circos-plots
Circular genome visualizations for displaying multiple data tracks around chromosome ideograms. | Tool | Language | Best...
requesting-code-review
Dispatch superpowers:code-reviewer subagent to catch issues before they cascade. Core principle: Review early, review of...
bio-data-visualization-upset-plots
library(UpSetR) upset(fromExpression(data), order.by = 'freq', nsets = 6) genesets <- list( SetA = c('Gene1', 'Gene2', '...
bio-small-rna-seq-target-prediction
miranda miRNA.fa UTRs.fa \ -sc 140 \ -en -20 \ -out predictions.txt import pandas as pd def parsemiranda(outputfile): ''...
bio-phasing-imputation-imputation-qc
bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%INFO/DR2\t%INFO/AF\n' \ imputed.vcf.gz > infoscores.txt bcftools quer...
matchms
Matchms is an open-source Python library for mass spectrometry data processing and analysis. Import spectra from various...
bio-ribo-seq-riboseq-preprocessing
Reference examples tested with: Bowtie2 2.5.3+, STAR 2.7.11+, cutadapt 4.4+, numpy 1.26+, pysam 0.22+, samtools 1.19+ Be...
pdf-processing
Use pdfplumber to extract text from PDFs: import pdfplumber with pdfplumber.open("document.pdf") as pdf: text = pdf.page...
bio-copy-number-gatk-cnv
Reference examples tested with: GATK 4.5+ Before using code patterns, verify installed versions match. If versions diffe...
test-driven-development
Write the test first. Watch it fail. Write minimal code to pass. Core principle: If you didn't watch the test fail, you ...
docx-official
A user may ask you to create, edit, or analyze the contents of a .docx file. A .docx file is essentially a ZIP archive c...
bio-data-visualization-color-palettes
| Type | Use Case | Example | |------|----------|---------| | Sequential | Continuous data (expression, coverage) | viri...
geopandas
GeoPandas extends pandas to enable spatial operations on geometric types. It combines the capabilities of pandas and sha...
bio-genome-intervals-bed-file-basics
BED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates. BED3: chr start e...
shap
SHAP is a unified approach to explain machine learning model outputs using Shapley values from cooperative game theory. ...
bio-data-visualization-specialized-omics-plots
This skill provides reusable plotting functions for common omics visualizations that can be applied across different ana...
tooluniverse-proteomics-analysis
Comprehensive analysis of mass spectrometry-based proteomics data from protein identification through quantification, di...