Scripts I have written as a graduate research assistant
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Updated
Apr 16, 2024 - Python
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.
Interrogating the influence of Transposable Element insertions on transcriptional dynamics
Scripts I wrote as a graduate research assistant while working on the Wyeomyia smithii Genome project for Dr. Elizabeth Cooper's Lab at UNC Charlotte
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
Build your own deep learning transposable elements classifier with ease.
Tn3 Transposon/Toxin Finder
TE Classifier Using CNN
Composite Transposon Finder
A package to count reads mapping on transposable elements subfamilies, families and classes.
High-precision TE Annotator
A pipeline to to determine the repeat content of genes and their neighboring regions.
A tool to quantify transposable elements expression in scRNA-seq
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
Distribution of TEs and their relationship to genes in host genome
MCHelper: An automatic tool to curate transposable element libraries
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
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