Skip to main content

Table 2 Comparison of the functionalities of the different algorithms

From: RGmatch: matching genomic regions to proximal genes in omics data integration

  RGmatch Homer GREAT CisGenome Seq2pathway ChIPseeker
User − friendly Command line Command line Web tool Command line/GI (only in Windows) R/Bioc R/Bioc
Adaptable to pipelines Yes Yesa No Yesa Yesa Yesa
Input format BED (also gzip-compressed BED file) BED BED (only 3 columns) BED - > COD BED - > GRanges BED
Association resolution Gene, transcript, exon Gene, transcript Gene Gene Gene Gene, transcript
Area annotation Yes Yes No No Yes Yes
Flexibility Distance, Areas, Rules, Area priorities No Distance Distance Search radius Area priorities, TSS distance
Supported species All All 3 12 2 Allb
Output: Gene IDs? Any in the GTF Gene and transcript IDs Gene names Gene IDs Gene IDs and gene names Gene and transcript IDs
Output: Distance? Yes Yes Yes No Yes Yes
Output: Overlapping genes? Yes No No No Yes No
  1. aHOMER and CisGenome can be integrated in analysis pipelines, although the process to obtain the annotations and parse these results is not as straightforward as with RGmatch. Seq2pathway and ChIPseeker can also be integrated with additional scripting
  2. bIt supports all species, provided the input format is a TxDb R object. This format can be obtained from a GTF file by using the makeTxDbFromGFF function in the GenomicFeatures package