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bio-de-deseq2-basics
Reference examples tested with: DESeq2 1.42+, Salmon 1.10+, edgeR 4.0+, scanpy 1.10+ Before using code patterns, verify installed versions match. If v...
datamol
Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify complex molecul...
epigenomics-methylgpt-agent
The Epigenomics MethylGPT Agent leverages foundation models for comprehensive DNA methylation analysis. It integrates MethylGPT and DiffuCpG for methy...
tooluniverse-systems-biology
Comprehensive pathway and systems biology analysis integrating multiple curated databases to provide multi-dimensional view of biological systems, pat...
bio-restriction-sites
from Bio import SeqIO from Bio.Restriction import EcoRI, BamHI, HindIII, RestrictionBatch, Analysis record = SeqIO.read('sequence.fasta', 'fasta') seq...
nicheformer-spatial-agent
The Nicheformer Spatial Agent leverages the Nicheformer foundation model, trained on over 53 million spatially resolved cells, to model cellular archi...
bio-pathway-enrichment-visualization
Reference examples tested with: ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion('<pkg>...
agentd-drug-discovery
description (10-20 chars): Hypothesis foundry keywords: ligand-design, SAR, ADMET, docking, ranking measurableoutcome: Generate ≥10 candidate molecule...
bio-molecular-io
Reference examples tested with: RDKit 2024.03+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pack...
bio-crispr-screens-mageck-analysis
Reference examples tested with: MAGeCK 0.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+ Before using code patterns, verify installed versions match. If...
bio-reference-operations
Generate consensus sequences and manage reference files using samtools. Create index for random access to reference sequences. samtools faidx referenc...
markitdown
MarkItDown is a Python tool developed by Microsoft for converting various file formats to Markdown. It's particularly useful for converting documents ...