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Lokhorst, Wouter / BiG-SCAPE
GNU Affero General Public License v3.0Biosynthetic 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)
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Gebretsadkan, Samuel / BiG-SCAPE
GNU Affero General Public License v3.0Biosynthetic 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)
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Find SNPs in putative TFBS that change the expression of the nearby gene
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Simulation pipeline for generation of artificial polyploid genomes, estimation of their haplotypes from Next Generation Sequencing data using HapTree, HapCompass and SDhap, and finally evaluation of the estimation accuracy.
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A pipeline to align multiple whole genomes
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A convolutional neural network for the purpose of interpretable protein-protein interaction prediction.
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Scripts, data, and results used in the Master thesis of the student Antonio Luna de Haro in Wageningen UR
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Benden, Daniel / catchcam
GNU General Public License v2.0 or laterCatchCam is the software of the Catchcam hardware
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Willemsen, Johan / Happy-haplotype-assembly
GNU General Public License v3.0 onlyHappy - Haplotype assembly using Next-generation Sequencing (NGS) reads.
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Willemsen, Johan / Happy-haplotype-inference
GNU General Public License v2.0 or laterHappy - haplotype inference in polyploid species
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Family-based estimation of polyploid haplotypes using short sequence reads
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medema-group / biosyntheticSpadesRankingPipeline
GNU Affero General Public License v3.0Pipeline 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]
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