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molfeat
Molfeat is a comprehensive Python library for molecular featurization that unifies 100+ pre-trained embeddings and hand-crafted featurizers. Convert c...
bio-tumor-fraction-estimation
Reference examples tested with: CNVkit 0.9+, ichorCNA 0.5+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions diffe...
bio-genome-intervals-coverage-analysis
Calculate coverage and depth across genomic regions using bedtools and pybedtools. bedtools genomecov -ibam alignments.bam -bg > coverage.bedGraph bed...
bio-de-results
Reference examples tested with: DESeq2 1.42+, edgeR 4.0+ Before using code patterns, verify installed versions match. If versions differ: R: packageVe...
bio-workflows-longread-sv-pipeline
Complete workflow for detecting structural variants from ONT or PacBio long-read data. Long reads (ONT/PacBio) [1. QC] ----------------> NanoPlot [2. ...
bio-immunoinformatics-epitope-prediction
Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <package...
tooluniverse-rnaseq-deseq2
Comprehensive differential expression analysis of RNA-seq count data using PyDESeq2, with integrated enrichment analysis (gseapy) and gene annotation ...
bio-workflows-rnaseq-to-de
Complete pipeline from raw FASTQ files to differential expression results. FASTQ files [1. QC & Trimming] -----> fastp [2. Quantification] ----> Salmo...
bio-paired-end-fastq
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pac...
scanpy
Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows incl...
multi-ancestry-prs-agent
The Multi-Ancestry PRS Agent provides AI-optimized polygenic risk score calculation designed to work across diverse ancestral populations. It addresse...
molecular-glue-discovery-agent
The Molecular Glue Discovery Agent enables AI-driven discovery of molecular glue degraders that induce protein-protein interactions between E3 ligases...