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bio-restriction-mapping
from Bio import SeqIO from Bio.Restriction import EcoRI, BamHI, HindIII, RestrictionBatch, Analysis record = SeqIO.read('sequence.fasta', 'fasta') seq...
scientific-schematics
Scientific schematics and diagrams transform complex concepts into clear visual representations for publication. This skill uses Nano Banana 2 AI for ...
torch_geometric
PyTorch Geometric is a library built on PyTorch for developing and training Graph Neural Networks (GNNs). Apply this skill for deep learning on graphs...
bio-phasing-imputation-genotype-imputation
java -jar beagle.jar \ gt=study.vcf.gz \ ref=referencepanel.vcf.gz \ map=geneticmap.txt \ out=imputed java -Xmx32g -jar beagle.jar \ gt=study.vcf.gz \...
bio-metabolomics-msdial-preprocessing
Reference examples tested with: numpy 1.26+, pandas 2.2+, scanpy 1.10+, xcms 4.0+ Before using code patterns, verify installed versions match. If vers...
MAGE
Run the MAGE antibody generation workflow to propose antigen-conditioned antibody sequences for downstream structural validation. Prep env: cd repo an...
anndata
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs), variable...
pydeseq2
PyDESeq2 is a Python implementation of DESeq2 for differential expression analysis with bulk RNA-seq data. Design and execute complete workflows from ...
bio-single-cell-lineage-tracing
Reference examples tested with: Cassiopeia 2.0+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+ Before using code patterns, verify installed versions matc...
bio-single-cell-splicing
Reference examples tested with: anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+ Before using code patterns, verify installed versions match. If ...
tooluniverse-proteomics-analysis
Comprehensive analysis of mass spectrometry-based proteomics data from protein identification through quantification, differential expression, post-tr...
bio-data-visualization-specialized-omics-plots
This skill provides reusable plotting functions for common omics visualizations that can be applied across different analysis types: Volcano plots (an...