Table 2.
Overview of IR detection/quantification algorithms
| Tool/Resource | Purpose/method | Website | Reference |
|---|---|---|---|
| IRFinder | Detecting IR from RNA-Seq experiments | github.com/williamritchie/IRFinder | (16) |
| Kma | R package for IR detection | github.com/pachterlab/kma | (125) |
| MISO | (Differential) gene isoform expression analysis; determines intronic percent spliced in (PSI) levels | genes.mit.edu/burgelab/miso | (127) |
| rMATS | Differential AS analysis | rnaseq-mats.sourceforge.net | (134) |
| spliceR | AS identification/quantification | bioconductor.org/packages/spliceR | (164) |
| IntEREst | IR quantification | github.com/gacatag/IntEREst | (126) |
| Psichomics | AS quantification and analysis | bioconductor.org/packages/psichomics | (135) |
| Whippet | Fast AS detection and quantification algorithm | github.com/timbitz/Whippet.jl | (165) |
| SUPPA2 | Fast differential splicing analysis | github.com/comprna/SUPPA | (136) |
| MAJIQ | Detection and quantification of local splicing variations from RNA-Seq data | majiq.biociphers.org | (166) |
| VAST-TOOLS | Toolset for profiling and comparing AS events in RNA-Seq data | github.com/vastgroup/vast-tools | (137) |
| ASTALAVISTA | AS quantification and analysis | astalavista.sammeth.net | (138) |
| JUM | AS quantification and analysis | github.com/qqwang-berkeley/JUM | (141) |
| SpliceHunter | AS quantification and analysis | bitbucket.org/canzar/splicehunter | (32) |