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Table 1 Overview comparison of functionalities of Cistrome, CisGenome and SeqMINER

From: Cistrome: an integrative platform for transcriptional regulation studies

  Cistrome CisGenome 2 SeqMINER 1.2.1
Data preprocessing    
   ChIP-chip preprocessing Yes. Affymetrix or NimbleGen platform Yes. Affymetrix or other platform through conversions Not available
   ChIP-seq preprocessing Yes Yes. No support for SAM/BAM Not available
   General peak calling Yes. Through wiggle file for signals No direct solution Not available
   Cross-platform analysis Yes. Across different ChIP-chip platforms, or across different ChIP-seq libraries Not available Not available
Expression analysis    
   From normalization, differential expression, to gene ontology Yes. Affymetrix or NimbleGen platform Not available Not available
Integrative analysis    
   Genome association study Yes. Chromosome or gene feature enrichment; aggregation plot; genes or peaks centered annotation; conservation plot; k-means clustering heatmap Yes. Closest genes around peaks Yes. K-means clustering at peak sites; interactive heatmap; aggregation plot
   Correlation between samples Yes. Whole genome or peak centered Pearson correlation; Venn diagram Not available Yes. Pearson correlation at enriched regions
   Motif analysis Yes. Find enriched known or de novo motifs; map motifs to genomic locations Yes. Find de novo motifs; map motifs to genomic locations Not available
Other tools Liftover both BED/WIGGLE files; low level operations on text manipulation and format conversion through Galaxy Many useful scripts for format conversions, to calculate overlaps and so on Not available
Genome browser visualization Redirect to mirrored UCSC genome browser on Cistrome, or external genome browsers supported by Galaxy Local installed genome browser on Windows operating system Not available