Explore projects

Detect specific sequences in nanopore squiggles, no basecalling required

Scripts and files for data preparation

Scripts and files for data analysis of dataset 1 (by Roxann) - behaviour and spatial data

Repo for dataset 2 (milk production and activity from 10 farms)

Diverse python helper-functies voor algemeen gebruik, maar met name richting MNP management, voor het team Biodiversiteit en Beleid. Door: Levi Biersteker & Hans Roelofsen.

Analysis code repository for the minor thesis project at BIF group. Topic: Using machine learning to predict underlying factors for plant meiotic recombination rate variation Supervisor: Aalt-Jan van Dijk

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.

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency Index)

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency Index)

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard index, a modified Domain Duplicate Score and the Goodman-Kruskal gamma function)

Pipeline to rank multiple putative BGC assemblies as those generated by biosyntheticSpades when there are multiple possible paths in the assembly graph. Code is derived by an early version of BiG-SCAPE [https://git.wur.nl/medema-group/BiG-SCAPE]

A concept for a BrAPI discovery node. Written in Python, Flask-based.

BSc Thesis Erik IJland