Curated List of Biomarkers, Blood Tests, and Blood Tracking

R package for microbiome biomarker discovery

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

Learn interpretable computational phenotyping models from k-merized genomic data

OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.

TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images

Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

👀 An all-purpose eye tracking web application and API for Alzheimer's disease research (3 tasks, <3 mins). 1st place in the 2021 CNT hackathon https://www.cnthackathon.org/

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Python implementation of the feature relevance interval (FRI) algorithm

Investigating the reproducibility of federated GNN models

FS-Select identifies the best feature selection (FS) method for a given dataset from a pool of FS methods.

netNorm (network normalization) framework for multi-view network integration (or fusion), recoded up in Python by Ahmed Nebli.

We provide both Matlab and Python versions of netNorm. In this folder you find the Maltab version of the code.

This repository is the author implementation of the paper "Biomarker Identification by Reversing the Learning Mechanism of Autoencoder and Recursive Feature Elimination"

📦 🔬 R/biotmle: Targeted Learning with Moderated Statistics for Biomarker Discovery

Multimodal Context-Aware Detection of Glioma Biomarkers using MRI and WSI