Curated List of Biomarkers, Blood Tests, and Blood Tracking

R package for microbiome biomarker discovery

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.

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

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

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

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

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

Single cell analysis using Low Resource

👀 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/

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

Investigating the reproducibility of federated GNN models

Python implementation of the feature relevance interval (FRI) algorithm

CimpleG, an R package to find (small) CpG signatures.

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

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

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

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