Figure 4

ChIPseeqer graphical interface. (A) The users can control all parameters of the tools. For example, in the Find Pathway tool (the GUI version of ChIPseeqerPathwayMatch) the user can select: the input peaks, the species of their data, the gene annotation database used to extract the genes related to the input peaks, which subset of the peaks to include in the analysis (e.g., promoter peaks, intergenic peaks), and which pathways database to use in order to look for the pathway. The desired pathway can be either selected from a list of available pathways or typed by the user (e.g., apoptosis, development). (B) The typical output of each tool is a table summarizing all peaks resulting from the analysis, as well as basic statistics (e.g., how many peaks found). Here, the peaks that contain the TCCTAGA motif are shown, after using the Find Motif in peaks tool (the GUI version of ChIPseeqerMotifMatch). (C) Several tools also provide graphical output. For example, the summary result of iPAGE tool (the GUI version of ChIPseeqeriPAGE) is a pathway enrichment table showing the level of enrichment for all pathways found in the genes related to the input peaks (category 1), compared to the genes used as background (category 0). (D) The output of the Similarity coefficient tool (the GUI version of ChIPseeqerComputeJaccardIndex) is a color-coded matrix, showing the pairs of datasets that have more common peaks than others, with darker red color.