Software
Software: Quicklinks
Taxonomic Analysis
Analysis of (Multi-)Omics Data
Pangenomic Analysis
Transcriptome Architecture Analysis
Dimensionality Reduction
Software in Detail
(Ancient) Genomic Analysis
With EAGER, we provide an intuitive and user-friendly way for researchers to address two problems in current ancient genome reconstruction projects.
Summarize SNV and indel information on single gene or genome level together with other relevant statistics based on .vcf files.
Reveal is our visual analytical approach to the challenges of eQTL data exploration and visualization.
mitoBench is an integrated workbench for mitochondrial data analysis, incorporating several state of the art visualization methods and accompanying data handling tools for easier analysis.
Improving Ancient DNA Assembly
inPHAP is our interactive phased haplotype visualization tool, featuring a variety of interaction possibilities such as zooming, sorting, filtering and aggregation of rows in order to explore patterns hidden in large genetic datasets.
Our Genome Profile Alignment tool GPA relies on progressiveMauve for the underlying alignment, to compute several smaller sets of aligned genomes that are combined to a full WGA through their profiles. The computation of the profiles of the WGAs and their merging is conducted by using the SuperGenome data structure.
Taxonomic Analysis
Interactive visual analytics tool for the simultaneous exploration of phylogenetic relationships, genome-wide SNP data and metadata.
BLASTphylo is an interactive web-tool, which applies a BLASTp search for a given protein and maps the result on a given taxonomic tree. In addition, a phylogeny calculation of the remaining BLAST hits can be performed and visualized.
Analysis of (Multi-)Omics Data
Mayday is a microarray data analysis platform and is designed to be a flexible solution for processing microarray data. It features interactive visualization as well as a plug-in framework to support analytical tools.
An interactive visualization tool developed to address the limitations of current visualization approaches in the multi-omics field. The tool consists of an automated part that clusters omics data to determine trends and an interactive visualization.
Interactive visualization of GO enrichments results for different omics data.
An R-shiny app that allows interactively using the DeSeq2 R package in a user-friendly web app without any programming expertise.
Pangenomic Analysis
Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.
Alignment visualization based on SuperGenome coordinates.
Transcriptome Architecture Analysis
Comparative TSS prediction from RNA-seq data.
nocoRNAc is a software for the automated prediction and characterization of ncRNA transcripts in bacterial genomes.
Dimensionality Reduction
VIPurPCA offers a visualization of uncertainty propagated through the dimensionality reduction technique Principal Component Analysis (PCA) by automatic differentiation.