Software

eVIP

https://github.com/BrooksLabUCSC/eVIP2

Expression variant impact phenotyping (eVIP) is an approach to predict functional impacts of mutations by comparing gene expression signatures induced by wild-type vs. mutated ORFs.

Associated manuscripts:

    • eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants. Alexis M. Thornton, Lishan Fang, April Lo, Maria McSharry, David Haan, Casey O’Brien, Alice H. Berger , Marios Giannakis , Angela N. Brooks. PLoS Comput Biol. 2021 Jul 2;17(7):e1009132. doi: 10.1371/journal.pcbi.1009132. PMID: 34214079; PMCID: PMC8281988.
    • An expression-based variant impact phenotyping protocol to predict the impact of gene variants in cell lines
      Thornton AM, Tumu M, Brooks AN. STAR Protocols 2022. https://doi.org/10.1016/j.xpro.2022.101651

 

FLAIR

https://github.com/BrooksLabUCSC/flair

FLAIR (Full-Length Alternative Isoform analysis of RNA) for the alignment correction, isoform definition, and alternative splicing analysis of long-reads.

Associated manuscripts:

    • Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
      Tang AD, Soulette CM, van Baren MJ, Hart K, Hrabeta-Robinson E, Wu CJ, Brooks AN.
      Nature Communications. 2020 Mar 18;11(1):1438. doi: 10.1038/s41467-020-15171-6.
    • Nanopore native RNA sequencing of a human poly(A) transcriptome
      Rachael E. Workman*, Alison D. Tang*, Paul S. Tang*, Miten Jain*, John R. Tyson*, Roham Razaghi*, Philip C. Zuzarte, Timothy Gilpatrick, Alexander Payne, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Goes de Jesus, Karen L. Jones, Cameron M. Soulette, Terrance P. Snutch, Nicholas Loman, Benedict Paten, Matthew Loose, Jared T. Simpson, Hugh E. Olsen**, Angela N. Brooks**, Mark Akeson**#, Winston Timp**# *Contributed equally to the work, **Co-lead the project, #Corresponding authors.
      Nature Methods. 2019 Dec; 16(12):1297-1305. doi: 10.1038/s41592-019-0617-2

JuncBASE

https://github.com/anbrooks/juncBASE

JuncBASE is used to identify and classify alternative splicing events from RNA-Seq data. Alternative splicing events are identified from splice junction reads from RNA-Seq read alignments and annotated exon coordinates. In addition to the identification of alternative splicing events. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples. JuncBASE was originally developed to characterize annotated and novel alternative splicing events throughout Drosophila development as well as splice events that are altered upon knockdown of splice factors. It has been further developed and used for alternative splicing analysis in cancer RNA-Seq studies.

Associated manuscripts:

    • Conservation of an RNA Regulatory Map between Drosophila and Mammals
      Brooks AN*, Yang L*, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, and Graveley BR
      Genome Research, 21:193-202
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