Tools
Tools, software and resources
Tools, software and databases we develop and maintain
WHALE
A bioinformatics pipeline based on Nextflow and nf-core for long-read DNA sequencing analysis.
https://github.com/TBLabFJD/WHALE
PARROT
A bioinformatics nextflow pipeline for DNASeq analysis optimized for WGS and rare diseases.
https://github.com/TBLabFJD/PARROT-FJD
VIsoQLR
An interactive tool for the detection, quantification and fine-tuning of isoforms using long-read sequencing.
https://github.com/TBLabFJD/VIsoQLR
PriorR
Graphical filtering and prioritization program for genomic variants analysis.
https://github.com/TBLabFJD/PriorR
GLOWgenes
A network-based algorithm for the prediction of gene-diasease associations. Designed to be used in the prioritization of candidate genes in WES and WGS analysis of rare diseases.
EPICv2-methylation-analysis
A bioinformatics pipeline for epiegentics using EPICv2 array
https://github.com/TBLabFJD/EPICv2-methylation-analysis
NextVariantFJD
DNASeq analysis designed for rare disease diagnosis (CES, WES, WGS) and implemented in nextflow.
https://github.com/TBLabFJD/NextVariantFJD
PTMcode
Database for known and predicted functional associations between protein post-translational modifications (PTMs).
Machine learning R code
https://github.com/pminguez/MachineLearning4UnbalancedData
Snow (Studying Networks in the Omic World)
Extracts the protein-protein interaction networks behind a list of genes/proteins (signature) and evaluates its robutness against same-size networks generated from random lists of genes/proteins.
Babelomics
We are part of the consortium that develops Babelomics (http://babelomics.org), an on-line platform for an integral analysis of transcriptomic experiments, from raw data, normalization, differential expression, clustering, machine learning and other statistical analyses to the functional profiling using classical, gene set and network approaches.
more on ... https://github.com/TBLabFJD
We also contributed somehow to other tools (in some of their releases)
STRING
Protein-protein interaction networks.
OGEE (database of Online GEne Essentiality)
http://ogeedb.embl.de
Old tools and databases we developed or contributed to ..
Tissues Mining Tool
Finds tissues and tissue histologies in which two lists of genes display different distributions.
MarmiteScan
Use chemical and disease related information to detect related blocks of genes in a gene list with associated values.
Marmite
Finds differential distributions of bioentities extracted from PubMed between two groups of genes.
AtEnsembl
The Arabidopsis thaliana Genome browser.