Welcome to the GENIE Python package

Introduction

The GENIE project provides mutation data for a large number of patients and cancer indications. However, many different panels are used for generating the data, and these panels have different coverage of tested genomic ranges. Therefore, to get the mutation profile of genes across samples it needs to be checked whether a particular genomic region is tested by a panel. If a sample is tested with a panel not covering a region of interest, the mutational status of this sample is unknown.

The genie package provides means to get mutation profiles of genes for all samples where the gene has actually been tested. Such profiles can then also be used to estimate the frequency of mutations in a disease indication.

Please see also some comments on the GENIE data for observations that I made while working on this package.