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Table 1 The main tools of the ChIPseeqer framework.

From: An integrated ChIP-seq analysis platform with customizable workflows

Tool name Description GUI availability
QcAnalysisTools Offers basic quality control tools. NA
ChIPseeqerSplitReadFiles Splits read files (e.g., bed, eland) into one read file per chromosome.
ChIPseeqer Peak detection algorithm.
ChIPseeqerSummaryPromoters Creates a promoters-based annotation of the detected peaks (i.e., gene name-description, peaks)
ChIPseeqerAnnotate Finds the peaks distribution in the genome (e.g., exons/introns/intergenic) and creates lists of these peaks.
ChIPseeqerPeaksTrack Creates a UCSC Genome Browser track for the detected peaks.
ChIPseeqerMakeReadDensityTrack Creates a UCSC Genome Browser track for the reads density.
ChIPseeqerNongenicAnnotate Finds the peaks that overlap with repeating elements, CpG islands and segmental duplicates.
ChIPseeqerFIRE Runs FIRE for the detected peaks, in order to perform an unsupervised motif discovery.
ChIPseeqerMotifMatch Runs MyScanACE for the detected peaks, in order to look for specific motifs (Jaspar, Bulyk PBM databases).
ChIPseeqeriPAGE Runs PAGE for the genes associated with the detected peaks, in order to perform pathways analysis.
ChIPseeqerPathwayMatch Looks for genes (and their corresponding peaks) that are associated to a specific pathway (e.g., apoptosis, GO:0060742).
ChIPseeqerCons Estimates the conservation scores for the detected peaks and for random intervals to allow comparison.
ChIPseeqerDensityMatrix Creates a reads density matrix for a window around the TSS or the TES of the genes, or for any interval selected. NA
ChIPseeqerReadCountMatrix Estimates the avg/max reads number for every input peak, across multiple ChIP-seq datasets and creates a peak-based reads matrix. NA
ChIPseeqerCluster Clusters a matrix (e.g., k-means, hierarchical, SOMs) and visualizes the clustering. NA
CompareIntervals Compares two lists of peaks and finds the overlapping peaks and the peaks that are unique in each list.
CompareGenes Compares two lists of genes and finds the common genes and the genes that are unique in each list.
ChIPseeqerComputeJaccardIndex Estimates the Jaccard similarity coefficient for a set of peak files. The larger the coefficient, the more similarity you have between two peak files
ChIPseeqerMakeGenepartsMatrix Creates gene-based matrices (one for promoters, one for exons, etc) for many peak files. Summarizes the number of peaks that fall in specific gene parts, across many different peak files (TFs). NA
ChIPseeqerFindDistalPeaks Finds peaks that are away from known genes. NA
ChIPseeqerFindClosestGenes Finds the closest gene(s) for each peak. NA
ChIPseeqerGetReadCountInPeakRegions Estimates the avg/max reads number for every peak, for a ChIP-seq dataset and creates a peak-based read matrix. NA
FindPeaksWithMotif Extracts the peaks that have a specific FIRE motif (can be applied after running FIRE). NA
MakePAGEInput Creates the input file for iPAGE from a list of genes. NA
  1. The table shows the names of the tools, short description of their functionality and their availability within the ChIPseeqer interface. This is not an exhaustive list; all available tools are documented online [37].