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
Pipeline for Transposable Elements Locus Level Analysis.
A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis
Find and classify transposable elements using convolutional neural networks.
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.
A pipeline to to determine the repeat content of genes and their neighboring regions.
Uncertainty-aware quantification of 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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