(1) Installation and Quick-Start

This section provides instructions for installation and a quick working example to demonstrate the important functions of NxtIRF. NxtIRFcore is the command line utility for NxtIRF.

For detailed explanations of each step shown here, refer to chapter 2: “Explaining the NxtIRF workflow” in this vignette. For a list of ready-made “recipes” for typical-use NxtIRF in real datasets, refer to chapter 3: “NxtIRF cookbook”


To install NxtIRFcore, start R (version “4.1”) and enter:

(Optional) For MacOS users, make sure OpenMP libraries are installed correctly. We recommend users follow this guide, but the quickest way to get started is to install libomp via brew:

Building the NxtIRF reference

A NxtIRF reference requires a genome FASTA file (containing genome nucleotide sequences) and a gene annotation GTF file (preferably from Ensembl or Gencode).

NxtIRF provides an example genome and gene annotation which can be accessed via the NxtIRFdata package installed with NxtIRF:

Using these two files, we construct a NxtIRF reference as follows:

Running IRFinder

NxtIRF provides an example set of 6 BAM files to demonstrate its use via this vignette.

Firstly, retrieve the BAM files from ExperimentHub using the NxtIRF helper function NxtIRF_example_bams(). This makes a copy of the BAM files to the temporary directory:

Finally, run NxtIRF/IRFinder as follows:

Collate individual IRFinder runs to build a NxtIRF Experiment

First, collate the IRFinder output files using the helper function Find_IRFinder_Output()

This creates a 3-column data frame with sample name, IRFinder gzipped text output, and COV files. Compile these output files into a single experiment:

Importing the collated data as a NxtSE object:

The NxtSE is a data structure that inherits SummarizedExperiment