Codes and key processed files for Xie et al. manuscript
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Codes and scripts used in Xie et al. manuscript IMPORTANT NOTE: the biomarkers and algorithms in this repo are protected by multiple patents. The codes could only be used for academic evaluations, distributed under the [CC BY-NC-ND 4.0](https://creativecommons.org/licenses/by-nc-nd/4.0/ "CC BY-NC-ND") license. Please contact Dr. Kun Sun (sunkun@szbl.ac.cn) for enquiries about commercial usages. Our programs/codes were developed on a CentOS v7.5 (64-bit, kernal version v3.10.0) machine with the following software and packages: - Ktrim v1.6.0; - Bowtie2 v2.3.5.1; - Bedtools v2.29.2; - R v4.1.2, requires "ggplot2", "ggpubr", "ggprism", "reshape2", "forcats", "ggbeeswarm", "dplyr", "cowplot", "tidyverse", "verification", "gbm", "caret", "foreach", "doParallel", "binom", and "pROC" packages. CfDNA data processing For raw cfDNA read processing, including preprocessing, alignment, and duplicate removal, please refer to Liu et al. STAR Protocols 2025 (https://www.sciencedirect.com/science/article/pii/S2666166725001637) and this https://github.com/hellosunking/STAR-Protocol-cfDNA-end-selection. CfDNA feature extractions 1. For size, end selection and motif features, please refer to Ju et al. Cell Reports Methods 2024 (https://www.sciencedirect.com/science/article/pii/S2667237524002601), Liu et al. STAR Protocols 2025 (https://www.sciencedirect.com/science/article/pii/S2666166725001637), and this https://github.com/hellosunking/STAR-Protocol-cfDNA-end-selection. 2. For E-index, please refer to An et al. Nature Communications 2023 (https://www.nature.com/articles/s41467-023-35959-6) and https://github.com/hellosunking/STAR-Protocol-cfDNA-end-selection. 3. Programs for copy number analysis, including extracting mean and s.d. values from the reference panel, calculating read counts per bin and converting to Z-scores, are provided in `Copy.number` directory. We first analyzed the referece panel to calculcate mean and sd values for each 5Mb genomic bin using `1.calc.mean.sd.in.reference/process.reference.sh`, and generated `1.calc.mean.sd.in.reference/Prostate.reference.bin5M.mean.sd` file; then we calculated the Z-scores for each sample per bin using `2.calc.z.score/calc.Zscore.sh`. 4. Programs for analyzing AR-specific binding regions, including region definition and extracting cfDNA signals, are provided in `AR-specific.binding.regions` directory. You need to prepare a `bed.list` file and then run `2.profile.cfDNA/profile.cfDNA.sh` to get the features. 5. Programs for calculating RSD (relative sequencing depth) values for TEs are provided in `RSD` directory. You need to prepare a `bed.list` file and then run `calc.RSD.sh` to get the features. Building PROTECTOR and PROTECTOR+ models Programs and feature matrices for building PROTECTOR and PROTECTOR+ models are provided in `PROTECTOR.model` directory. Run `build.PROTECTOR.models.sh` to build the models and plot ROC curves.
