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bio-clip-seq-clip-motif-analysis
bedtools getfasta -fi genome.fa -bed peaks.bed -fo peaks.fa findMotifs.pl peaks.fa fasta outputdir \ -len 6,7,8 \ -rna meme-chip -oc outputdir \ -dna ...
liquid-biopsy-analytics-agent
The Liquid Biopsy Analytics Agent provides comprehensive AI-driven analysis of blood-based cancer biomarkers. It integrates circulating tumor DNA (ctD...
bio-workflow-management-snakemake-workflows
Compatible with Snakemake 7.x, 8.x, and 9.x. For Snakemake 8.0+, use --executor instead of --cluster. rule all: input: expand("results/{sample}counts....
gnomad-database
The Genome Aggregation Database (gnomAD) is the largest publicly available collection of human genetic variation, aggregated from large-scale sequenci...
nk-cell-therapy-agent
The NK Cell Therapy Agent provides AI-driven design and optimization of natural killer cell therapies for cancer treatment. It covers CAR-NK engineeri...
scvi-tools
scvi-tools is a comprehensive Python framework for probabilistic models in single-cell genomics. Built on PyTorch and PyTorch Lightning, it provides d...
mrd-edge-detection-agent
The MRD-EDGE Detection Agent implements the MRD-EDGE (Enhanced Detection of ctDNA through Genomic Error suppression) deep learning algorithm for ultra...
bio-spatial-transcriptomics-spatial-deconvolution
Reference examples tested with: anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+ Before using code patterns, verify installed ve...
bio-workflows-microbiome-pipeline
Paired-End FASTQ (16S V4) ┌──────────────────────────────────────────────────┐ │ microbiome-pipeline │ ├─────────────────...
deep-research
Autonomous multi-step research that searches multiple sources, reads full content, synthesizes findings, and produces a structured report. User wants ...
biomni
Biomni is an open-source biomedical AI agent framework from Stanford's SNAP lab that autonomously executes complex research tasks across biomedical do...
tooluniverse-drug-target-validation
Validate drug target hypotheses using multi-dimensional computational evidence before committing to wet-lab work. Produces a quantitative Target Valid...