IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

TY - JOUR

T1 - IsoformSwitchAnalyzeR

T2 - analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

AU - Vitting-Seerup, Kristoffer

AU - Sandelin, Albin

N1 - © The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected].

PY - 2019/11/1

Y1 - 2019/11/1

N2 - Summary: Alternative splicing is an important mechanism involved in health and disease. Recent work highlights the importance of investigating genome-wide changes in splicing patterns and the subsequent functional consequences. Current computational methods only support such analysis on a gene-by-gene basis. Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform switches. As a case study, we analyzed RNA-seq data from The Cancer Genome Atlas and found systematic changes in alternative splicing and the consequences of the associated isoform switches. Availability and implementation: Windows, Linux and Mac OS: http://bioconductor.org/packages/IsoformSwitchAnalyzeR. Supplementary information: Supplementary data are available at Bioinformatics online.

AB - Summary: Alternative splicing is an important mechanism involved in health and disease. Recent work highlights the importance of investigating genome-wide changes in splicing patterns and the subsequent functional consequences. Current computational methods only support such analysis on a gene-by-gene basis. Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform switches. As a case study, we analyzed RNA-seq data from The Cancer Genome Atlas and found systematic changes in alternative splicing and the consequences of the associated isoform switches. Availability and implementation: Windows, Linux and Mac OS: http://bioconductor.org/packages/IsoformSwitchAnalyzeR. Supplementary information: Supplementary data are available at Bioinformatics online.

U2 - 10.1093/bioinformatics/btz247

DO - 10.1093/bioinformatics/btz247

M3 - Journal article

C2 - 30989184

SN - 1367-4803

VL - 35

SP - 4469

EP - 4471

JO - Bioinformatics

JF - Bioinformatics

IS - 21

ER -