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Table 1 Comparison of selected software tools for ChIP-Seq data analysis

From: jChIP: a graphical environment for exploratory ChIP-Seq data analysis

Application Interface Installation Platform Functionality Pros Cons
UCSC genome browser [7] web-based not needed platform independent genome browsing, tracks displaying, tracks comparing, referring to known genomic features no installation, graphical interface, rich annotation database batch process of a large number of data files not possible
BEDTools [6] command-line compilation from source through package managers UNIX LINUX MacOS interrogation and manipulation of genomic features, comparisons of discontinuous features fast, divided into several applications no graphical interface,
HOMER [3] command-line Perl installation scripts UNIX LINUX MacOS Cygwin data visualisation, peak and enriched motif finding, assembling data across multiple experiments, annotating peaks, basic quality control (sequence bias, fragment length estimation), creating histograms, and heatmaps, re-centering peaks on motifs fast, divided into several applications, multiple additional scripts helpful by analysis no graphical interface
ChipSeeker [5] R package through R package manager platform independent (R package needed) data visualisation, peak detection, pathways enrichment analysis, retrieving the nearest genes around the peak, genomic region annotation, peak significance estimation, conservation analysis, clustering analysis, data comparison with GEO database interaction with other R packages, R environment required, programming skill needed
CisGenome [4] GUI (MS Windows only) command line compilation from source installer (for MS Windows) packages for all platforms (GUI only for MS Windows) peak detection, gene annotation, motif analysis, motif mapping, novel motif discovery, data visualisation GUI (MS Windows only), divided into several applications no graphical interface (Linux, UNIX, MacOS)
jChIP GUI not required platform independent (Java runtime environment required) data visualisation, matching reads to genomic locations, datasets comparision, creating reads count histograms, basic quality control no installation, graphical interface only exploratory analysis available