Boas Pucker

teaching. This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

PythonTUBS. Python introduction for life scientists

MGSE. Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

AppliedGenomeResearch. course about NGS data processing: genomics and transcriptomics

APPLS. Applied Python Programming for Life Scientists

RNA-Seq_analysis. scripts for RNA-Seq analysis

PlantBioinformatics. Materials of the course WBIO-A-08 Plant Bioinformatics

MolecularMethodsInGenomeResearch. practical course about lab methods in genome research

MYB_annotator. 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.

FlavonoidFriday. Flavonoids are specialized metabolites in plants that have numerous functions including protection against abiotic stresses, pigmentation, and repelling herbivores.This repository provides additional background to the #FlavonoidFriday tweets

KIPEs. Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new transcriptome of genome sequence assembly.

PyBo. Python for Life Scientists at the University of Bonn

MybMonday. MYB transcription factors are one of the largest gene family in plants and control many processes. This repository provides additional background to the #MYB_Monday tweets

PlantGenomicsGuide. Instructions for all major step in a plant genome sequencing project

script_collection. Collection of scripts to solve small bioinformatic challenges.

NAVIP. Neighborhood-Aware Variant Impact Predictor

yam. scripts associated with yam genome assembly

LRG. Long Read Genomics course materials

ncss2018. Genome-wide investigation of non-canonical splice sites

ToolOverview. summary of available plant genomics tools

AppliedPlantTranscriptomics. Collection of materials belonging to the Applied Plant Transcriptomics course

LongReadWalker. closing gaps in long read assemblies by long read walking

Overview. Overview of repositories associated with @bpucker & @PuckerLab. This covers science communication projects, the developed bioinformatics tools, teaching activities, and project specific repositories.

bHLH_annotator. automatic annotation of bHLH gene family in plants

GenomeAssembly. collection of tools for the analysis and cleaning of genome assemblies

CHS. CHS gene structure prediction analysis

bananaMYB. scripts associated with the genome-wide analysis of MYBs in the banana genome

teaching_concepts. Teaching concept collection

Boas_Pucker. Homepage of Boas Pucker listing publications and professional activities

variant_calling. variant calling and processing

CoExpPhylo. Collection of scripts associated with co-expression and phylogenetic analysis approach

PBBtools. collection of mini tools for the BioinfToolServer

RepeatsInBeets. phylogenetic generalized least square (PGLS) regressions for repeats and genome sizes in beets

phyl_constr. construction of species tree based on large sequence data sets

AppliedPlantGenomics. materials and scripts used for Applied Plant Genomics

MtMYBs. scripts associated with the genome-wide investigation of MYBs in Medicago

yam_scripts. all my yam scripts

GKseq. scripts for Arabidopsis thaliana resequencing analyses

vivi-bud-dev. collection of scripts related to the bud development study in Vitis vinifera

Nd1_PacBio. scripts associated with the Nd-1 genome assembly based on PacBio data

CoExp. Co-Expression analysis tool

CacaoGenomics. scripts associated with the Theobroma cacao genome sequencing project

RNAseqQualCheck. script to assess the quality of RNAseq data sets

lycocyc. collection of scripts for lycopene cyclase analysis

DataLiteracyInPlantSciences. scripts and data sets associated with Data Literacy in Plant Sciences course

ApiaceaeFNS1. FNS I evolution in Apiaceae

pbb-wetlab. wet lab methods used in the group

BnaGeneticMarkers. analysis and mapping of genetic markers in Brassica napus

banana_transcriptomics. scripts associated with banana transcriptomics

codon_usage. script associated with codon usage

orthogroups. script related to the filtering and analysis of orthogroups in the Caryophyllales

spark. Python

AhaGenome. script associated with A. halleri genome assembly