Welcome

This guide will walk you through analysis of NULISAseq proteomic data using R.

If you have limited experience with R or prefer a graphical user interface, consider using the NULISA Analysis Software (NAS) — a cloud-based platform designed for intuitive data processing, visualization, and analysis.

What is NULISAseqR?

NULISAseqR is an R package designed specifically for working with NULISAseq proteomic data. It provides:

Data Import: Read XML files from NULISAseq multiplex proteomic panels
Quality Control: Automated QC metrics and reporting
Visualization: Heatmaps, PCA plots, volcano plots, boxplots, etc.
Statistical Analysis: Differential abundance testing and longitudinal analysis
Outcome Modeling: Linear models using single-protein abundance to predict an outcome

Installation

New to R? If you haven’t installed R and RStudio yet, see the Installing R and RStudio guide in the Additional Resources page.

macOS Users

Important: Before installing NULISAseqR on macOS, you need to install Xcode Command Line Tools:

Install Xcode from the App Store (if not already installed)
Open Terminal and run this code to accept the Xcode license agreement:

sudo xcodebuild -license accept

Windows Users

Important: Before installing NULISAseqR on Windows, you need to install Rtools which provides compilers and utilities to build packages from source:

Go to https://cran.r-project.org/bin/windows/Rtools/
Download and install the appropriate Rtools version for your R installation
Follow the installation instructions on the website

Installation Steps

Follow these steps to install NULISAseqR and its dependencies:

# 1. Install devtools
if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")

# 2. Install BiocManager for Bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

# 3. Install ComplexHeatmap from Bioconductor
BiocManager::install("ComplexHeatmap")

# 4. Install ggalt from CRAN snapshot
install.packages('ggalt', repos = "http://packagemanager.posit.co/cran/2025-08-02")

# 5. Install PCAtools (Alamar fork)
devtools::install_github('Alamar-Biosciences/PCAtools')

# 6. Install NULISAseqR
devtools::install_github('Alamar-Biosciences/NULISAseqR')

# 7. Install additional packages for data analysis
install.packages("tidyverse")
install.packages("table1")
install.packages("pROC")

Note: If you encounter issues installing packages from source, you may need to restart R (Cmd/Ctrl + Shift + F10 in RStudio) between major installation steps.

Load the packages:

library(NULISAseqR)
library(tidyverse)

Getting Help

Function help: Type ?function_name in the R console
GitHub Issues: Report bugs or request features

NULISAseqR User Guide