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bio-machine-learning-biomarker-discovery

Identifies all features that are significantly better than random (shadow features). from boruta import BorutaPy from sklearn.ensemble import RandomFo...

by FreedomIntelligence

github 4 files

bio-machine-learning-omics-classifiers

from sklearn.modelselection import traintestsplit from sklearn.preprocessing import StandardScaler from sklearn.pipeline import Pipeline from sklearn....

by FreedomIntelligence

github 4 files

bio-machine-learning-prediction-explanation

import shap from sklearn.ensemble import RandomForestClassifier model = RandomForestClassifier(nestimators=100, randomstate=42) model.fit(Xtrain, ytra...

by FreedomIntelligence

github 4 files

bio-machine-learning-survival-analysis

from lifelines import KaplanMeierFitter import matplotlib.pyplot as plt kmf = KaplanMeierFitter() kmf.fit(T, eventobserved=E) kmf.plotsurvivalfunction...

by FreedomIntelligence

github 4 files

bio-metabolomics-lipidomics

Reference examples tested with: ggplot2 3.5+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, xcms 4.0+ Before using code patterns, verify installed versions ...

by FreedomIntelligence

github 3 files

bio-metabolomics-normalization-qc

Reference examples tested with: xcms 4.0+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion('<pkg>') ...

by FreedomIntelligence

github 3 files

bio-metabolomics-statistical-analysis

Reference examples tested with: R stats (base), ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packa...

by FreedomIntelligence

github 3 files

filtering-best-practices

Is dataset large enough for VQSR? (>30 exomes or WGS) ├── Yes → Use VQSR (machine learning) └── No → Use hard filters ├── Germline → GATK recommended ...

by FreedomIntelligence

github 3 files

medical-imaging-review

Write comprehensive literature reviews following a systematic 7-phase workflow. Initialize project with three core files: CLAUDE.md - Writing guidelin...

by FreedomIntelligence

github 6 files

tooluniverse-chemical-safety

Comprehensive chemical safety and toxicology analysis integrating predictive AI models, curated toxicogenomics databases, regulatory safety data, and ...

by FreedomIntelligence

github 3 files

proteinmpnn

| Requirement | Minimum | Recommended | |-------------|---------|-------------| | Python | 3.8+ | 3.10 | | CUDA | 11.0+ | 11.7+ | | GPU VRAM | 8GB | 1...

by FreedomIntelligence

github 2 files

bio-clinical-databases-clinvar-lookup

Reference examples tested with: Entrez Direct 21.0+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: P...

by FreedomIntelligence

github 3 files