SummarizedExperiment
A container class to represent genomic experiments in Python; follows Bioconductor’s SummarizedExperiment.
LiquidBayes
LiquidBayes is a Bayesian Network (BN) for inferring tumour fraction and clonal prevalences from whole genome sequencing of cell-free DNA (cfDNA) and Direct Library Preparation (DLP+) of a matched tissue biopsy.
stpt2imc
Deep learning model implemented using PyTorch to reconstruct Imaging Mass Spectrometry (IMC) images from Serial Two-Photon Tomography (STPT).
MethylationDPGMM
Dirichlet Process Gaussian Mixture Model (DPGMM) for multi-modal pan-cancer stratification using DNA methylation and RNA expression.
Regression Application
A Python GUI app developed using PyQt5 software. Uses statsmodels to perform different types of regressions. Visualizes regressions with matplotlib. User friendly UI that is easy to use and pleasant to look at.