Earl Grey: A fully automated TE curation and annotation pipeline
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Updated
Aug 26, 2024 - Python
Earl Grey: A fully automated TE curation and annotation pipeline
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
High-precision TE Annotator
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
MCHelper: An automatic tool to curate transposable element libraries
Distribution of TEs and their relationship to genes in host genome
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq
A pipeline to to determine the repeat content of genes and their neighboring regions.
A package to count reads mapping on transposable elements subfamilies, families and classes.
Composite Transposon Finder
TE Classifier Using CNN
Build your own deep learning transposable elements classifier with ease.
Tn3 Transposon/Toxin Finder
Find and classify transposable elements using convolutional neural networks.
A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis
Useful python scripts for genomic analyses
Scripts I have written as a graduate research assistant
A pipeline for identification and annotation of transposable element (TE) insertions using next generation sequencing (NGS) data.
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