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