Gene Set Enrichment Analysis Made Awesome

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further in…

Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1

Short pipelines for NGS data analysis

Omics data integration with o2plsda

A tool to minimize storage utilization for omics data.

Toolkit for omics network analysis and predictive modeling

Specifications and validators for omics data formats used on C. autoethanogemum C1 program

A Generative Discriminative Framework that Integrates Imaging, Genetic, andDiagnosis Data into Coupled Low Dimensional Space

A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

The command line interface and client library for DNAstack services and GA4GH-compatible service, implemented in Python

This code automates aligning similar peaks across different mass spect runs based on a user specified m/z tolerance value

R-package for structural equation modeling based on GWAS summary data

Probabilistic OPLS discriminant analysis

This repo summaries the main bioinformatics tools.

Data and code associated with the Parkinson's Disease review paper by Schilder, Navarro & Raj (2021).

Teaching materials for Introduction to ‘–omics’

Code scripts for ’Prediction of overall survival in stage II and III Colon Cancer through Machine Learning of Rapidly-acquired Proteomics‘

Find and classify transposable elements using convolutional neural networks.