MaizeStressDB is a robust data exploration tool tailored for the analysis of gene expression profiles in maize leaves under three distinct stresses: Cold, Dry, and Heat. Offering access to a comprehensive collection of 120 samples across 10-time points for each stress condition, MaizeStressDB empowers researchers with versatile tools for expression analysis, differential gene expression, and network exploration.

DiMmer is a Java tool for efficient processing of Illumina 450K and 850K EPIC chip data. It is fully parallelizable and can process even big cohort data sets. With DiMmer, one may now even compute empirical p-values using permutation tests and find differentially methylated regions including different strategies for correction for multiple testing. It can correct for cell composition effects and other confounders. Continuous outcome variables and confounders can be directly integrated using regression models. It comes with an intuitive user interface that guides the clinician or biologist through all steps of a typical Illumina EWAS chip data analysis.

HitSeekR is the first web platform for analyzing high-throughput screening (HTS) data of various types, from miRNA (inhibitor) screens and RNAi assays to CRISPER/cas9 and drug response screens. It can accommodate, normalize, etc. small to ultra-large scale, and it turns your HTS data into a systems biology story.

Transitivity Clustering is a tool for solving the Weighted Graph Cluster Editing Problem using a force-based heuristic. It comes with several extensions. TransClustMV, for instance, works with missing values.

ClustEval is a platform for the evaluation of clustering tools in many different biomedical settings.

MIRACLE is an online platform for microarray R-based analysis of complex lysate experiments. It is bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation.

With the DeepCLIP online tool you can choose one or more trained state-of-the-art performing models and use them to generate predictions and binding profiles of RNA-sequences of interest. Both predictions and binding profiles can detect how mutations may change the affinity of RNA-binding proteins for analyzed sequences.

CoNVaQ is a web service for CNV-based association study between two or more sample groups. The web interface allows one to quickly upload segmented CNV samples and search for variations that are overrepresented in a population. CoNVaQ differs from previous tools by allowing you to specify which CNVRs are considered significant using simple queries, e.g. “find the largest region duplicated in > 70% of cases and < 10% of controls”.

BALSAM is a comprehensive web-platform to simplify and automate the analysis and discovery of metabolite patterns in Multi-Capillary-Column Ion-Mobility-Spectrometry data. It combines preprocessing, peak detection, feature extraction, visualization and pattern discovery.

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IMSDB is database system and machine learning user interface for biomarker mining and identification in breath data from GC/MS and MCC/IMS data sets.

PIPS is a tool specifically for the prediction of pathogenicity islands using sequence features.

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GIPSy extends on the PIPS idea and implements a software for using genomic features to predict pathogenicity islands as well metabolic and resistance islands in bacterial genomes.

OpenLabFramework with its extension OpenLabNotes is an open-source laboratory information management system (LIMS) intended for advanced sample management in small to mid-sized laboratories. It has been developed with focus on the management of vector clone and genetically engineered cell lines.