FAQ

1. What are the system requirements for installing RWireX?

RWireX requires R (version 4.1 or higher) and depends on several packages including ArchR (>= 1.0.1), SpectralTAD (>= 1.16.1), and plotgardener (>= 1.6.2). It can be installed using the devtools package from GitHub.

2. What data formats are supported by RWireX?

RWireX is compatible with ArchR-processed scATAC-seq data, supporting various experimental designs and cell populations. It can work with both single-cell and aggregated (metacell) data formats within the ArchR framework.

3. Where can I find test data for RWireX?

Test data are available for download as part of RWireX. Have a look at the Test data wiki entry. These are useful for running example workflows and validating your setup. The test data can also be directly accessed from Zenodo.

4. How does RWireX handle background co-accessibility?

RWireX computes background co-accessibility for each sample separately to account for sample-specific noise and biases. We recommend using the 99th percentile of background co-accessibility from shuffled accessibility matrices as a lower cutoff to filter for true-positive co-accessible links. This helps distinguishing genuine co-accessibility from random associations.