These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
6. The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data. Schuierer S; Roma G Nucleic Acids Res; 2016 Sep; 44(16):e132. PubMed ID: 27302131 [TBL] [Abstract][Full Text] [Related]
7. 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]
9. iMapSplice: Alleviating reference bias through personalized RNA-seq alignment. Liu X; MacLeod JN; Liu J PLoS One; 2018; 13(8):e0201554. PubMed ID: 30096157 [TBL] [Abstract][Full Text] [Related]
10. Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using the Coxe T; Burks DJ; Singh U; Mittler R; Azad RK Plants (Basel); 2024 Feb; 13(5):. PubMed ID: 38475429 [TBL] [Abstract][Full Text] [Related]
11. RNA-Seq read alignments with PALMapper. Jean G; Kahles A; Sreedharan VT; De Bona F; Rätsch G Curr Protoc Bioinformatics; 2010 Dec; Chapter 11():Unit 11.6. PubMed ID: 21154708 [TBL] [Abstract][Full Text] [Related]
12. JAGuaR: junction alignments to genome for RNA-seq reads. Butterfield YS; Kreitzman M; Thiessen N; Corbett RD; Li Y; Pang J; Ma YP; Jones SJ; Birol İ PLoS One; 2014; 9(7):e102398. PubMed ID: 25062255 [TBL] [Abstract][Full Text] [Related]
13. FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions. Gatto A; Torroja-Fungairiño C; Mazzarotto F; Cook SA; Barton PJ; Sánchez-Cabo F; Lara-Pezzi E Nucleic Acids Res; 2014 Apr; 42(8):e71. PubMed ID: 24574529 [TBL] [Abstract][Full Text] [Related]
14. RNASequel: accurate and repeat tolerant realignment of RNA-seq reads. Wilson GW; Stein LD Nucleic Acids Res; 2015 Oct; 43(18):e122. PubMed ID: 26082497 [TBL] [Abstract][Full Text] [Related]
15. Prediction and Quantification of Splice Events from RNA-Seq Data. Goldstein LD; Cao Y; Pau G; Lawrence M; Wu TD; Seshagiri S; Gentleman R PLoS One; 2016; 11(5):e0156132. PubMed ID: 27218464 [TBL] [Abstract][Full Text] [Related]
16. EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes. Shinder I; Hu R; Ji HJ; Chao KH; Pertea M Nat Commun; 2023 Nov; 14(1):7223. PubMed ID: 37940654 [TBL] [Abstract][Full Text] [Related]
18. Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length. Lou SK; Li JW; Qin H; Yim AK; Lo LY; Ni B; Leung KS; Tsui SK; Chan TF BMC Bioinformatics; 2011; 12 Suppl 5(Suppl 5):S2. PubMed ID: 21988959 [TBL] [Abstract][Full Text] [Related]
19. SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data. Chu C; Li X; Wu Y BMC Bioinformatics; 2015; 16 Suppl 17(Suppl 17):S10. PubMed ID: 26678515 [TBL] [Abstract][Full Text] [Related]