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 for the integration of proteomics and transcriptomics data. The tool consists of an automated part that clusters omics data to determine trends in the combined data sets and an interactive visualization.
Comparative visualization of GO enrichments results from multiple lists of genes.
An R-shiny app that allows interactively using the DeSeq2 R package in a user-friendly web app without any programming expertise.
Pangenomic Analysis
PanGee is a software tool that computes the PanGenome from a given whole genome alignment (WGA). The computation refines homologous genes groups through a subsequent Reciprocal Best Hit-BLAST approach. For this, we make use of the SuperGenome data structure that offers the possibility to efficiently detect aligned homologs in the WGA.
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.
Whole genome alignment visualization based on SuperGenome coordinates. Whole-genome alignments elucidate similarity and diversity on different scales, GenomeRing highlights both similarity and variation of the genome architecture of a species. Its is mainly developed for bacterial genomes.
Transcriptome Architecture Analysis
Comparative Transcription Start Site (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.