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 |