This repository contains codes, scripts and notebooks for the Meningomyelocele de novo mutation project.
The pipeline to perform processing of the WXS sequencing data can be found in https://github.com/Gleeson-Lab/wxs_pipeline.
Quality control for kinship analysis can be found in https://github.com/Gleeson-Lab/MM_DNM/tree/main/DNM/Kindship.
De novo SNV detection from HaplotypeCaller to VQSR, variant annotation can be found in https://github.com/Gleeson-Lab/MM_DNM/tree/main/DNM.
Pipelines for computing the consensus regions can be found in https://github.com/Gleeson-Lab/MM_DNM/tree/main/Consensus_region.
De novo variant calling from WXS and WGS can be found in https://github.com/Gleeson-Lab/WGS_DNM.
Notebooks and scripts for spatial transcriptomic analysis with MERFISH can be found in https://github.com/Gleeson-Lab/MM_DNM/tree/main/MERFISH.
Notebook to process ScTyping for spatial transcriptomic analysis with MERFISH can be found in https://github.com/Gleeson-Lab/MM_DNM/blob/main/MERFISH/plot_cell_comp.r.
Code to conduct the DNM burden analysis can be found in https://github.com/Gleeson-Lab/MM_DNM/tree/main/DNM_burden_analysis.
Code to conduct the network colocalization can be foudn in https://github.com/Gleeson-Lab/MM_DNM/tree/main/Network, and network propagation analysis can be found in https://github.com/Gleeson-Lab/MM_DNM/tree/main/Network%20propagation
Code to plot MERFISH expression data can be found in https://github.com/Gleeson-Lab/MM_DNM/blob/main/MERFISH/plot_cell_comp.r, to plot clustering data can be found in https://github.com/Gleeson-Lab/MM_DNM/blob/main/MERFISH/MM_DNM_Cluster-Plotting.ipynb.
Code to plot functional experiments can be found in https://github.com/Gleeson-Lab/MM_DNM/tree/main/Functional%20experiment.
📧 Joseph Gleeson: jogleeson@health.ucsd.edu