From: Cistrome: an integrative platform for transcriptional regulation studies
 | Cistrome | CisGenome 2 | SeqMINER 1.2.1 |
---|---|---|---|
Data preprocessing | Â | Â | Â |
   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 | Â | Â | Â |
   From normalization, differential expression, to gene ontology | Yes. Affymetrix or NimbleGen platform | Not available | Not available |
Integrative analysis | Â | Â | Â |
   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 |