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Here you can find information on installation, functions and vignettes on how to run the RWireX workflows.
RWireX computes co-accessibility by Pearson correlation between genomic sites across different cell populations and at varying levels of resolution to identify both autonomous links of co-accessibility (ACs) and domains of contiguous co-accessibility (DCs).
The single cell co-accessibility workflow workflow identifies ACs from stochastic accessibility changes in ATAC peaks with a homogeneous population of single cells as input. Pearson correlation coefficients between two peaks are assessed against a local background model. Background co-accessibility is determined from the 99th percentile of co-accessibility from accessibility matrices per chromosome shuffled over cells and peaks. The stability of ACs is assessed from their prevalence in the single cell population by computing the average percent accessible cells of the linked peaks.
The “metacell co-accessibility” workflow identifies DCs from perturbed accessibility changes in genomic tiles and aggregated metacell profiles of cells with similar chromatin accessibility profiles. It requires cell populations that are heterogeneous in respect to a perturbation or cell type/state. This allows to identify broader genomic patterns of depleted or enriched co-accessibility along the genomic coordinate.
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