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L1_Project

This repository contains the L1 datasets used in the study, code and processed data for the paper in revision "Human L1 Transposition Dynamics Unraveled with Functional Data Analysis".

The study is broadly separated into three major parts

  1. Genome-wide visualization and distance analysis of the three L1 datasets (de novo L1s, polymorphic L1s, and human-specific L1s) included in the study
  2. Comparison of genomic landscape features related to L1 insertion and fixation via Interval-Wise Testing for Omics Data (IWTomics)
  3. Quantification of contribution from individual genomic features and their joint effect using Functional Logistic Regression (FLR) models

Folders

Datasets/: Genomic coordinates of elements from the three L1 datasets, their 100-kb flanking regions, and a control set

Analysis/: Contains analysis scripts and processed RData objects used to generate the results