Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

Earl Grey: A fully automated TE curation and annotation pipeline

A pipeline to detect chimeric transcripts derived from genes and transposable elements.

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4

Distribution of TEs and their relationship to genes in host genome

MCHelper: An automatic tool to curate transposable element libraries

High-precision TE Annotator

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq

A pipeline for identification and annotation of transposable element (TE) insertions using next generation sequencing (NGS) data.

Wrapper script to identify TEs and mask genome

Composite Transposon Finder

A pipeline to to determine the repeat content of genes and their neighboring regions.

A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis

Tn3 Transposon/Toxin Finder

Scripts I have written as a graduate research assistant

TE Classifier Using CNN

Build your own deep learning transposable elements classifier with ease.

This repository provides the code for identifying potential LTR retrotransposon tandem loci.

Interrogating the influence of Transposable Element insertions on transcriptional dynamics

Find and classify transposable elements using convolutional neural networks.