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PanTools, WUR Bioinformatics

Repository for Python raster GIS library with low memory requirements

HPC Deployment toolbox used at WUR for Anunna

A simple template repository for python projects

The script focuses on assessing tree vitality trends in urban areas of the Netherlands using high-resolution satellite data and vegetation indices. It employs tree segmentation, trend analysis with weighted linear regression, and classification based on slope values. The methodology enables scalable monitoring of tree health and stress, providing valuable insights for urban forestry management and planning.

A package that prepare video recordings to be used by deeplabcut (simple 2D/3D tracking, cropping and stitching). Then use deeplabcut to estimate the 2D coordinates of various bodyparts of a flying insect and fit a 3D skeleton to these 2D coordinates

Contains Instructions how to set up iRODS for sysadmins and training material for different user goups.

Postprocessing --

CNN methods that estimate the diameter of the crop, even when it's occluded.

Scripts and resources used for my MSc Thesis at the Bioinformatics chair group.

The goal this project is to create a pipeline that automates the secondary metabolite phylogenetic analysis of fungi to a certain extent.

Arabidopsis eQTL analysis platform

A script for retrieval of SMILES chemical data of compounds produced by Biosynthetic Gene Clusters. Data is gathered from the MIBiG repository (single package with all entries in JSON format)

Calculate the diversity of your gene clusters! Using hmmscan to find the pfam domains. Jaccard, DDS, GK as distance metrics including sequence similarity as a modifier. It outputs tab delimited network files that can be visualized in Cytoscape.

BAIT - a tool for breakpoint analysis and inference of time series

video machinelearning using yolov3 on windows 10

This project is containing some code and data for the tutorial on 3D plant phenotyping at the Summerschool on Application of Machine Learning in Plant Sciences, 12–16 September 2022, Einsiedeln, Switzerland.

Multiple protein structure alignment and feature extraction suite