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Starred repositories
PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics
A few tools for converting contact maps to .hic format compatible with the 4D Genome Browser.
A fast and efficient tool for converting chromatin interaction data between genome assemblies
k-mer learning materials
A pipeline to merge 2 or more sample SV VCFs into a consensus set and annotate with frequency resources with merging via jasmine
Ultra-fast preprocessing and quality control for long-read sequencing data
Splice junction analysis and filtering from BAM files
A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction
Posterior summarisation in Bayesian phylogenetics
tree visualization for tree + annotation data
My collection of light bioinformatics analysis pipelines for specific tasks
Analysis of monococcum introgressions into hexaploid wheat
A tool for discovering transposable elements and describing patterns of genome evolution
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
Methods and recipes for Plant Genome Annotation - Transposable Elements
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
In this study, we introduce MegaLTR, a robust online server that identifies intact LTR -RTs in any target genome, and its local standalone version. MegaLTR is freely available at https://bioinforma…
A generative AI extension for JupyterLab
Pipe Viewer - monitor the progress of data through a pipe. mirror of https://codeberg.org/a-j-wood/pv