Hailey Napier Duke University 10/22/22 - 12/16/22
This repository will serve as documentation for the computational aspects of my rotation project in the Eroglu Lab (10/22/22 - 12/16/22).
See my labarchives folder ("Hailey N. Oct 2022" in the "Rotations Students" directory within Kristina Sakers's labarchives notebook) for full descriptions of experiments and analysis.
- r_scripts contains only r scripts
- chromhmm_scripts contains r scripts used to analyze and create plots for chromhmm data and data related to chromatin states/chd8 binding
- chd8_overlap_wt_ko.R is a script to find overlap between chd8 binding sites and chromatin states
- get_chd8_binding_genes.R is a script to find the genes chd8 binds and their associated GO terms
- make_bam_binarization_files.R is a script to format the files for binarization for chromhmm
- image_analysis contains r scripts used to quantify image analysis and make plots for image analysis data
- 20221206_Cx43_image_analysis.R is a script to analyze connexin43 puncta
- chromhmm_scripts contains r scripts used to analyze and create plots for chromhmm data and data related to chromatin states/chd8 binding
- shell_scripts contains shell scripts I ran on DCC
- chd8_peaks_intersect_KO_WT.sh is a script to find the overlap of chd8 binding with chromatin states
- nlgn2_chromhmm.sh is a script to find chromatin states using mintchip .bed files from nlgn2 KO astrocytes
- backup_scripts.sh is a script to backup DCC shell files on my local computer (to be run on local terminal, not DCC)
Contact [email protected] with questions.