isv 0.3.0

Automated Interpretation of Structural Copy Number Variants

ISV package

Python package for easy prediction of pathogenicity Copy Number Variants (CNVs)

---

Requirements

xgboost>=1.4.2
shap>=0.39.0
sklearn-json>=0.1.0
numba>=0.53.1
numpy>=1.20.3
pandas>=1.2.4
numba>=0.53.1

The package might work with older versions, however above specified versions are recommended. Make sure to install these packages before installing the isv package

The package contains three functions:

1. isv.annotate(cnvs)

• annotates cnvs provided in a list, np.array or pandas DataFrame format represented in 4 columns: chromosome, start (grch38), end (grch38) and cnv_type
• Returns an annotated dataframe which can be used as an input to following two functions

2. isv.predict(X_raw, cnv_type, proba)

• returns an array of isv predictions

3. isv.shap_values(X_raw, cnv_type)

• calculates shap values for given CNVs