Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

Annotation helper tool for the manual curation of transposable element consensus sequences

An application to find and visualize circadian rhythms in time course data using extended harmonic oscillators.

R package specialized in HLA typing clustering and visualization based on specific similarity metrics

This is an R package to retrieve data from Open Target

APAlyzer is a toolkit for bioinformatic analysis of alternative polyadenylation (APA) events using RNA sequencing data. Our main approach is the comparison of sequencing reads in regions demarcated by high-quality polyadenylation sites (PASs) annotated in the PolyA_DB database (https://exon.apps.wistar.org/PolyA_DB/v3/). The current version (v3.…

Model-based analysis of APA using 3' end-linked reads

PenDA is a rank-based method for personalized differential analysis.

Repository containing source code, data, etc necessary to run Gene Set Analysis, Celltyping using MAGMA/Celltyping and Tissue Enrichment Analysis. Some of the formulas have been adapted from: NathanSkene/ALS_Human_EWCE, neurogenomics/EWCE, NathanSkene/MAGMA_Celltyping and jbryois/scRNA_disease github repositories.

Shiny App allows streamlined analysis of multiple levels of proteomics data.

BLASTr: an R package for parallel taxonomic classification of metabarcoding sequences

Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.

DRAGGER: Drug Repositioning by Analysis of GWAS and Gene Expression in R (maintained version). For publication version, see https://github.com/AEstebanMar/DAGGER-publication

Extract ITS and Neighboring Regions from Eukaryotic DNA Sequences

A clinical decision-support system for Age-Related Macular Degeneration (AMD) based on genetic and non-genetic features. The paper has been published in the Journal of Personalized Medicine.

A shiny app for simple heatmap based on ComplexHeatmap

An R-shiny interactive application to explore and valorise gene sets and lists from high throughput genomics experiments.

An ensemble of functions for easier and quicker preliminary microbiome analyses