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bulk-deseq2-analysis
Use this skill when a user wants to reproduce the DESeq2 workflow showcased in tdeseq2.ipynb. It covers loading raw featureCounts matrices, mapping En...
boltzgen
| Requirement | Minimum | Recommended | |-------------|---------|-------------| | Python | 3.10+ | 3.11 | | CUDA | 12.0+ | 12.1+ | | GPU VRAM | 24GB |...
myeloma-mrd-agent
The Myeloma MRD Agent provides comprehensive AI-driven minimal residual disease assessment for multiple myeloma. It integrates next-generation flow cy...
bio-imaging-mass-cytometry-phenotyping
Reference examples tested with: FlowSOM 2.10+, anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+ Before using ...
bio-variant-calling-deepvariant
Reference examples tested with: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: CLI: <tool>...
vcf-annotator
You are the VCF Annotator, a specialised agent for variant annotation and interpretation. VEP Annotation: Run Ensembl Variant Effect Predictor on VCF ...
rdkit
RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for readi...
tme-immune-profiling-agent
The TME Immune Profiling Agent provides comprehensive tumor microenvironment (TME) immune profiling by integrating multiple data modalities including ...
bio-machine-learning-model-validation
Simple train/test splits overestimate performance on small omics datasets. Nested CV provides unbiased estimates by separating hyperparameter tuning f...
neurokit2
NeuroKit2 is a comprehensive Python toolkit for processing and analyzing physiological signals (biosignals). Use this skill to process cardiovascular,...
tooluniverse-statistical-modeling
Comprehensive statistical modeling skill for fitting regression models, survival models, and mixed-effects models to biomedical data. Produces publica...
bio-microbiome-amplicon-processing
Reference examples tested with: DADA2 1.30+, cutadapt 4.4+ Before using code patterns, verify installed versions match. If versions differ: R: package...