Fig. 2.

An overview of the PLAIDOH pipeline and algorithm output. a Schematic of the single, input file required by PLAIDOH to identify all possible lncRNA/Coding gene Pairs (LCPs) in the user’s dataset. b Overview of the datasets that are used by PLAIDOH to annotate lncRNAs and predict activity based on genomic and epigenomic context. c Abridged example of the primary PLAIDOH output table, showing the three scores PLAIDOH calculates for each LCP as well as the 30+ additional columns of valuable information about the lncRNA and coding gene in each LCP. d Examples of graphs output by PLAIDOH as part of its standard run settings. The three LCPs and lncRNA1 diagrammed in a are highlighted in red and green, respectively