Services: software tools

A resource for analyzing and interpreting genetic dependencies in cancer.

Collection of tools for plant genome sequence analysis (MISA-web, Kmasker Plants, IPK BLAST server, BRIDGE).

Tool for analysis of molecular channels in proteins. CAVER Analyst allows interactive visualization of the channels and cavities in protein structures.

An R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.

A web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets

An R package used for efficient unraveling of the inherent dynamic properties of pathways.

Circlize is an R package used to generated circular visualization.

IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology.

A service oriented data mining tool

Multiple Sequence Alignment package via on-line server, in collaboration with groups in Germany, the UK and France.

ClustVis is a web tool for visualizing clustering of multivariate data. This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

A server for calculating contact maps of X-ray, NMR and predicted structures.

ComplexHeatmap is an R package which flexibly arranges multiple heatmaps and self define annotation graphics.

A tool to analyze structural ensembles of proteins by assessing their compliance to structural parameters derived from NMR measurements. Can be used both for ordered and disordered proteins and includes an option to select sub-ensembles with better correspondence to the parameters chosen.

Expertise on very diverse subjects of data processing, analysis and curation as well as connections to existing infrastructure RI's like EUDAT. This expertise can be made available to research projects and organisations.  

Aligns contigs from a draft genome to a closely related genome, and resolves their relative orientation based on this alignment.

Galaxy server allowing to align complete assemblies of SARS-CoV-2 genomes with the reference genomic sequence to obtain a list of polymorphic positions and to annotate genetic variants.

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

a web application that provides a graphical interface for Seurat version 2, a popular single-cell RNA-seq (scRNA-seq) package for R. It provides an easy-to-use UI and the ability to export results as an HTML file.

Domain based ANnotation of Transposable Elements (DANTE) uses database of Viridiplantae (Metazoa in progress) protein domains derived from transposable elements (Neumann at al 2019) Domains searching is accomplished engaging LASTAL alignment tool. Domains are subsequently annotated and classified using phylogenetic approach.

Research data management platform to enable researchers to produce FAIR data by design  

System for identification of alterations using protein mass spectrometry.

Prediction of protein sub-mitochondrial localization.

Prediction of secretory signal peptides and cleavage sites in proteins.

DELLY discovers germline and somatic structural variants in short-read massively parallel sequencing data

DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

An R-package used to extract disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments.

DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

OpenMS tool for targeted assay generation in metabolomics.