This is a repository to show my experience analyzing different kinds of Omics data.

Adversarial autoencoders for MHCI epitope and immunogenicity prediction

The documented analysis of the results reported in Akol et al., 2023 as R markdowns, Galaxy histories and jupyter logs..

Causal Inference Networks for Determining Expression Relationships Anthology

PhD thesis on data integration on inflammatory bowel disease

Code for the crb2a multi omics manuscript

Multi-omics differential dependency network inference

Multi-omics analysis of developing Rett Syndrome brain organoids

R Shiny application for the multi-omics analysis of inflammatory bowel disease

a multiomics approach on lung cancer (lung subtypes approach in https://github.com/arriagajorge/Lung-Cancer-Multi-Omics-subtype)

Hands-on experience in integrating and analyzing multi-omics data,using advanced bioinformatics tools to derive meaningful insights

PhD Thesis - Inferring effective cancer combination therapies using network-based multi-omics data integration

This is now the main repository. A few older issues are still tracked on gitlab for reference.

mND uses multi-layer Network Diffusion to find gene networks that contain high scoring genes. It considers two or more "layers" of genome-wide scores and an interactome.

Counting the number of publications related to specific keywords from the PubMed database over a range of years (2011-2024)

Testing RGCCA integration

Official repository for GeneLab AWGs

Network-based analysis of omics with multi-objective optimization

Supplementary code for the analysis of bridging with BsAb for BCMA CAR-T cell therapy in relapsed/refractory Multiple Myeloma.