158 related articles for article (PubMed ID: 37020334)
1. A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level.
Jiang M; Zhang S; Yin H; Zhuo Z; Meng G
Brief Bioinform; 2023 May; 24(3):. PubMed ID: 37020334
[TBL] [Abstract][Full Text] [Related]
2. Systematic evaluation of differential splicing tools for RNA-seq studies.
Mehmood A; Laiho A; Venäläinen MS; McGlinchey AJ; Wang N; Elo LL
Brief Bioinform; 2020 Dec; 21(6):2052-2065. PubMed ID: 31802105
[TBL] [Abstract][Full Text] [Related]
3. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.
Wang Y; Xie Z; Kutschera E; Adams JI; Kadash-Edmondson KE; Xing Y
Nat Protoc; 2024 Apr; 19(4):1083-1104. PubMed ID: 38396040
[TBL] [Abstract][Full Text] [Related]
4. Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.
Bai Y; Kinne J; Donham B; Jiang F; Ding L; Hassler JR; Kaufman RJ
BMC Genomics; 2016 Aug; 17 Suppl 7(Suppl 7):503. PubMed ID: 27556805
[TBL] [Abstract][Full Text] [Related]
5. One pipeline to predict them all? On the prediction of alternative splicing from RNA-Seq data.
Olofsson D; Preußner M; Kowar A; Heyd F; Neumann A
Biochem Biophys Res Commun; 2023 Apr; 653():31-37. PubMed ID: 36854218
[TBL] [Abstract][Full Text] [Related]
6. PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.
Lin KT; Krainer AR
Bioinformatics; 2019 Dec; 35(23):5048-5054. PubMed ID: 31135034
[TBL] [Abstract][Full Text] [Related]
7. Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods.
Quinn TP; Crowley TM; Richardson MF
BMC Bioinformatics; 2018 Jul; 19(1):274. PubMed ID: 30021534
[TBL] [Abstract][Full Text] [Related]
8. ASimulatoR: splice-aware RNA-Seq data simulation.
Manz Q; Tsoy O; Fenn A; Baumbach J; Völker U; List M; Kacprowski T
Bioinformatics; 2021 Sep; 37(18):3008-3010. PubMed ID: 33647976
[TBL] [Abstract][Full Text] [Related]
9. Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).
Sturgill D; Malone JH; Sun X; Smith HE; Rabinow L; Samson ML; Oliver B
BMC Bioinformatics; 2013 Nov; 14():320. PubMed ID: 24209455
[TBL] [Abstract][Full Text] [Related]
10. A comprehensive workflow for optimizing RNA-seq data analysis.
Jiang G; Zheng JY; Ren SN; Yin W; Xia X; Li Y; Wang HL
BMC Genomics; 2024 Jun; 25(1):631. PubMed ID: 38914930
[TBL] [Abstract][Full Text] [Related]
11. Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers.
Muller IB; Meijers S; Kampstra P; van Dijk S; van Elswijk M; Lin M; Wojtuszkiewicz AM; Jansen G; de Jonge R; Cloos J
BMC Bioinformatics; 2021 Jun; 22(1):347. PubMed ID: 34174808
[TBL] [Abstract][Full Text] [Related]
12. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).
Grant GR; Farkas MH; Pizarro AD; Lahens NF; Schug J; Brunk BP; Stoeckert CJ; Hogenesch JB; Pierce EA
Bioinformatics; 2011 Sep; 27(18):2518-28. PubMed ID: 21775302
[TBL] [Abstract][Full Text] [Related]
13. ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data.
Qi H; Guo X; Wang T; Zhang Z
Int J Mol Sci; 2022 Apr; 23(8):. PubMed ID: 35456896
[TBL] [Abstract][Full Text] [Related]
14. ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data.
Fry J; Li Y; Yang R
Bioinformatics; 2022 Oct; 38(21):4966-4968. PubMed ID: 36099042
[TBL] [Abstract][Full Text] [Related]
15. SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines.
Audoux J; Salson M; Grosset CF; Beaumeunier S; Holder JM; Commes T; Philippe N
BMC Bioinformatics; 2017 Sep; 18(1):428. PubMed ID: 28969586
[TBL] [Abstract][Full Text] [Related]
16. SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.
Pulyakhina I; Gazzoli I; 't Hoen PA; Verwey N; den Dunnen JT; Aartsma-Rus A; Laros JF
Nucleic Acids Res; 2015 Jul; 43(12):e80. PubMed ID: 25800735
[TBL] [Abstract][Full Text] [Related]
17. PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
Zhang Y; Lameijer EW; 't Hoen PA; Ning Z; Slagboom PE; Ye K
Bioinformatics; 2012 Feb; 28(4):479-86. PubMed ID: 22219203
[TBL] [Abstract][Full Text] [Related]
18. AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data.
Fahmi NA; Nassereddeen H; Chang J; Park M; Yeh H; Sun J; Fan D; Yong J; Zhang W
Int J Mol Sci; 2021 Apr; 22(9):. PubMed ID: 33922891
[TBL] [Abstract][Full Text] [Related]
19. A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies.
Merino GA; Conesa A; Fernández EA
Brief Bioinform; 2019 Mar; 20(2):471-481. PubMed ID: 29040385
[TBL] [Abstract][Full Text] [Related]
20. SplicingCompass: differential splicing detection using RNA-seq data.
Aschoff M; Hotz-Wagenblatt A; Glatting KH; Fischer M; Eils R; König R
Bioinformatics; 2013 May; 29(9):1141-8. PubMed ID: 23449093
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]