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
TE Classifier Using CNN
Build your own deep learning transposable elements classifier with ease.
Interrogating the influence of Transposable Element insertions on transcriptional dynamics
Find and classify transposable elements using convolutional neural networks.
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
Useful python scripts for genomic analyses
A package to count reads mapping on transposable elements subfamilies, families and classes.
Composite Transposon Finder
A pipeline for identification and annotation of transposable element (TE) insertions using next generation sequencing (NGS) data.
Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq
A pipeline to to determine the repeat content of genes and their neighboring regions.
High-precision TE Annotator
A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis
Tn3 Transposon/Toxin Finder
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
Distribution of TEs and their relationship to genes in host genome
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
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