NApy: Efficient Statistics in Python for Large-Scale Heterogeneous Data with Enhanced Support for Missing Data.

Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE.

Multi-omics regulatory network inference in the presence of missing data.

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Systematic analysis of alternative splicing in time course data using Spycone.

Cancer driver drug interaction explorer.

<i>SimBu</i>: bias-aware simulation of bulk RNA-seq data with variable cell-type composition.

Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.

A systematic comparison of novel and existing differential analysis methods for CyTOF data.

Machine learning for deciphering cell heterogeneity and gene regulation.

DIGGER: exploring the functional role of alternative splicing in protein interactions.

The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond.

ASimulatoR: splice-aware RNA-Seq data simulation.

BiCoN: network-constrained biclustering of patients and omics data.

On the limits of active module identification.

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

EpiRegio: analysis and retrieval of regulatory elements linked to genes.

Federated Multi-Mini-Batch: An Efficient Training Approach to Federated Learning in Non-IID Environments.

Privacy-preserving Artificial Intelligence Techniques in Biomedicine.

EpiGEN: an epistasis simulation pipeline.

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.

Large-scale inference of competing endogenous RNA networks with sparse partial correlation.

JAMI: fast computation of conditional mutual information for ceRNA network analysis.

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.

Ten Simple Rules for Developing Usable Software in Computational Biology.

Interactive microbial distribution analysis using BioAtlas.

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

DeepBlueR: large-scale epigenomic analysis in R.

KeyPathwayMinerWeb: online multi-omics network enrichment.

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

Robust<i> de novo</i> pathway enrichment with <i>KeyPathwayMiner 5</i>.

OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework.

Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data.

Microarray R-based analysis of complex lysate experiments with MIRACLE.