The landscape of allele-specific expression in human kidneys

This is the GitHub repository for the code used to analyze allele-specific expression in human kidneys.

Codes in this Github repository

1_rnaseq: Aligning RNA-seq reads to the reference genome using STAR, removing duplicates with samtools markdup and removing reference bias with WASP

2_phaser: Haplotype phasing using phASER and estimaing gene-level haplotypic counts using phASER geneAE

3_phaser: Transcript quantification using RSEM

4_toga: Resolving overlapping ASE genes and calling ASE Genes from phASER data.

5_imprinting: Use population-level ASE data to identify genomic imprinting candidates among genes.

ase_call: Alternative to 4_toga for calling ASE genes from gene-level haplotypic counts without our overlapping genes analysis.

rna_only_pipeline: Alternative to 1_rnaseq if only RNA-seq data present. Calling heterozygous variants from RNA-seq reads, optimized for ASE analysis

DEG_GSEA: Performing differential gene expression using DESeq2 and gene set enrichment analysis using clusterProfiler

Cell-Fraction: Estimating cell-type fraction of ASE genes using KPMP single cell RNA-seq data

Dependencies

This repository relies on R libraries, Python libraries, command line executables, and cloning github repositories to the local system.

1. Local Repository Dependencies:

In the same directory as this repository, clone phaser and RNA_Imprinting.

Repository structure:

[user ASE_NEPTUNE]$ ls ../
ASE_NEPTUNE  phaser  RNA_Imprinting

2. Command-Line Executables:

The following software packages must be installed on your system and accessible from the command line: STAR, bcftools, samtools, bedtools, rsem, tabix, gatk, picard

3. R Libraries:

The R libraries should be installed within your R environment: clusterProfiler, org.Hs.eg.dB, Seurat, SeuratDisk, DESeq2, tidyverse, optparse, data.table, R.matlab, hdf5r, rhdf5, arrow

4. Python Libraries:

These Python libraries are required: pandas, numpy, statsmodels, scipy

Reference

Ana C. Onuchic-Whitford†, Junmo Sung†, Eric D. Sakkas†, Michelle T. McNulty, Christopher L. O’Connor, Anya Greenberg, Jihoon G. Yoon, Sowmya Badina, NEPTUNE (Nephrotic Syndrome Study Network), Laura Mariani, Markus Bitzer, Matthew G. Sampson*, Dongwon Lee*. The landscape of allele-specific expression in human kidneys, BioRxiv, 2025

† These authors contributed equally to this work.

*Corresponding authors. Email: dongwon.lee@childrens.harvard.edu, matthew.sampson@childrens.harvard.edu