System requirements
Matlab (2021a) is required to be installed. 
Matlab is installed and ran under windows 11.

Installation guide
It typically takes 2-3 hours for the package installation and environment setting up.
Matlab can be installed according to the following instruction: 
https://www.mathworks.com/help/install/ug/install-products-with-internet-connection.html

Code and instructions for use

Code are stored in folder "1_DataAnalysisCode" and "2_LibraryDesignCode". 
Data are stored in folder "3_200LociData" and "4_ChromatinTracingData".

1. DataAnalysisCode: Raw images from different experiments are processed using code files organized by experiment type:

  1_General_Epi_PHR_SignalBackground: Contains codes for detecting FISH signals and quantifying the corresponding Epi-PHR signal-to-background ratio.

  2_200_Loci_Epi_PHR: Processes multiplexed FISH signals, decodes their identities, and measures the associated Epi-PHR signal-to-background ratios.

  3_500kb_CombinedChromatinTracing: Detects chromatin tracing FISH signals, reconstructs chromatin traces, and quantifies their Epi-PHR signal-to-background ratios.

  4_Dlk1_Meg3: Analyzes chromatin tracing FISH signals, reconstructs chromatin traces, measures Epi-PHR signal-to-background ratios, and phases these signals based on SNP FISH data.

2. LibraryDesignCode: Oligo libraries for different experiments are designed using code files grouped by experiment type:

  1_200_Gene_EpiPHR: Includes codes for processing DNA sequences, performing BLAST to filter low-quality oligos, and appending Epi-PHR docking sites and readout regions to selected DNA oligos.

  2_Dlk1_Meg3: Contains code for SNP FISH probe design, DNA sequence processing, BLAST-based filtering of poor oligos, and addition of Epi-PHR docking sites and readout regions to designated oligos.


