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 |