alternativeSplicingEvents: Alternative splicing annotation for AnnotationHub

In nuno-agostinho/alternativeSplicingEvents: Alternative splicing annotation for AnnotationHub

Description

Alternative splicing annotation for multiple species. These annotations are based on the VastDB files used by the alternative splicing quantification program VAST-TOOLS.

Details

Annotation data is available for the following species and assemblies:

• Homo sapiens (hg19, Hsa)

• Homo sapiens (hg38 Hs2)

• Mus musculus (mm9, Mmu)

• Mus musculus (mm10, Mm2)

• Bos taurus (bosTau6, Bta)

• Gallus gallus (galGal3, Gg3)

• Gallus gallus (galGal4, Gg4)

• Xenopus tropicalis (xenTro3, Xt1)

• Danio rerio (danRer10, Dre)

• Branchiostoma lanceolatum (braLan2, Bl1)

• Strongylocentrotus purpuratus (strPur4, Spu)

• Drosophila melanogaster (dm6, Dme)

• Strigamia maritima (strMar1, Sma)

• Caenorhabditis elegans (ce11, Cel)

• Schmidtea mediterranea (schMed31, Sme)

• Nematostella vectensis (nemVec1, Nve)

• Arabidopsis thaliana (araTha10, Ath)

The available alternative splicing event types include:

• Skipped exon

• Retained intron

• Alternative 3' splice site

• Alternative 5' splice site

Splicing events not assigned to any genes are marked as Hypothetical.

For more details, check the scripts/make-data.R file.

Source

https://github.com/vastgroup/vast-tools#vastdb-libraries

References

VAST-TOOLS: Irimia M, Weatheritt RJ, Ellis J, et al. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell. 2014;159(7):1511-1523.

nuno-agostinho/alternativeSplicingEvents documentation built on Dec. 22, 2021, 3:19 a.m.