For our tasks, we mainly use R and Bioconductor software packages.

We have developed the following software packages as part of our research:

• pcaExplorer (https://bioconductor.org/packages/pcaExplorer/), “Interactive Visualization of RNA-seq Data Using a Principal Components Approach”, doi.org/10.1186/s12859-019-2879-1

• ideal (https://bioconductor.org/packages/ideal/), “Interactive Differential Expression AnaLysis”, doi.org/10.1186/s12859-020-03819-5

• GeneTonic (https://bioconductor.org/packages/GeneTonic/), “GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data”, doi.org/10.1186/s12859-021-04461-5

• iSEE (https://bioconductor.org/packages/iSEE/), “iSEE: Interactive SummarizedExperiment Explorer”, doi.org/10.12688/f1000research.14966.1

• iSEEu  (https://bioconductor.org/packages/iSEEu/), “The iSEE Universe”

• simrec  (https://cran.r-project.org/package=simrec), “Simulating Recurrent Event Data with Hazard Functions Defined on a Total Time Scale”, doi.org/10.1186/s12874-015-0005-2

• annoFuse (https://github.com/d3b-center/annoFuse), “annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions”, https://doi.org/10.1186/s12859-020-03922-7

• TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), “TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation”, doi.org/10.1093/nar/gkaa722

• netmeta (https://cran.r-project.org/package=netmeta), “A graphical tool for locating inconsistency in network meta-analyses”, https://doi.org/10.1186/1471-2288-13-35

• SteppedPower (https://cran.r-project.org/package=SteppedPower), “Power Calculation for Stepped Wedge Designs”

• Rhineland-Palatinate Mortality Monitoring, http://shiny.imbei.uni-mainz.de:3838/rlp_mm/  

• GENEHUNTER-MODSCORE 4.0
• GENEHUNTER-MODSCORE 3.1.1
• GENEHUNTER-IMPRINTING
• GENEHUNTER-TWOLOCUS
• GENEHUNTER-QMOD