This is an overview of all github repositories associated with PuckerLab. Please find a list of the science communication projects, the developed bioinformatics tools, teaching activities, and project specific repositories below.

Specific facts and research projects about MYB transcription factors are shared on a weekly basis via Twitter and LinkedIn using #MybMonday. All posts are collected in the #MybMonday github repository.

Specific facts and research projects about the flavonoid biosynthesis are shared on a weekly basis via Twitter and LinkedIn using #FlavonoidFriday. All posts are collected in the #FlavonoidFriday github repository.

Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new transcriptome of genome sequence assembly. Scripts and datasets are availabe in the KIPEs repository. KIPEs is also available on our web server. This enables all scientists to use KIPEs in their research projects. Please find additional details in the corresponding publication 'Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium'. Recently, we updated KIPEs with additional features and data sets as described in our preprint 'KIPEs3: Automatic annotation of biosynthesis pathways'.

This tool performs an automatic identification, annotation, and analysis of the MYB gene family in plants. It can be applied to new transcriptome of genome assemblies. https://github.com/bpucker/MYB_annotator server publication

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly. https://github.com/bpucker/MGSE server publication

Prediction of the functional consequences of sequence variants listed in a VCF file. https://github.com/bpucker/NAVIP server (under construction) publication

Do you have questions or are you interested in a collaboration? Please get in touch via email.