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Items: 1 to 20 of 105


CRAC: an integrated approach to the analysis of RNA-seq reads.

Philippe N, Salson M, Commes T, Rivals E.

Genome Biol. 2013 Mar 28;14(3):R30. doi: 10.1186/gb-2013-14-3-r30.


MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.

Nucleic Acids Res. 2010 Oct;38(18):e178. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27.


TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.


Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U.

Genome Biol. 2010;11(3):R34. doi: 10.1186/gb-2010-11-3-r34. Epub 2010 Mar 17.


SplicingCompass: differential splicing detection using RNA-seq data.

Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, Eils R, König R.

Bioinformatics. 2013 May 1;29(9):1141-8. doi: 10.1093/bioinformatics/btt101. Epub 2013 Feb 28.


TrueSight: a new algorithm for splice junction detection using RNA-seq.

Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J.

Nucleic Acids Res. 2013 Feb 1;41(4):e51. doi: 10.1093/nar/gks1311. Epub 2012 Dec 18.


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 15;28(4):479-86. doi: 10.1093/bioinformatics/btr712. Epub 2012 Jan 4.


Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

Au KF, Jiang H, Lin L, Xing Y, Wong WH.

Nucleic Acids Res. 2010 Aug;38(14):4570-8. doi: 10.1093/nar/gkq211. Epub 2010 Apr 5.


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 15;27(18):2518-28. doi: 10.1093/bioinformatics/btr427. Epub 2011 Jul 19.


Discover hidden splicing variations by mapping personal transcriptomes to personal genomes.

Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y.

Nucleic Acids Res. 2015 Dec 15;43(22):10612-22. doi: 10.1093/nar/gkv1099. Epub 2015 Nov 17.


STAR: ultrafast universal RNA-seq aligner.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.

Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.


FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

Liu C, Ma J, Chang CJ, Zhou X.

BMC Bioinformatics. 2013 Jun 15;14:193. doi: 10.1186/1471-2105-14-193.


HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data.

Dimon MT, Sorber K, DeRisi JL.

PLoS One. 2010 Nov 8;5(11):e13875. doi: 10.1371/journal.pone.0013875.


IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data.

Bai Y, Ji S, Wang Y.

BMC Genomics. 2015;16 Suppl 2:S9. doi: 10.1186/1471-2164-16-S2-S9. Epub 2015 Jan 21.


A context-based approach to identify the most likely mapping for RNA-seq experiments.

Bonfert T, Csaba G, Zimmer R, Friedel CC.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S9. doi: 10.1186/1471-2105-13-S6-S9.


A probabilistic framework for aligning paired-end RNA-seq data.

Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J.

Bioinformatics. 2010 Aug 15;26(16):1950-7. doi: 10.1093/bioinformatics/btq336. Epub 2010 Jun 23.


PASTA: splice junction identification from RNA-sequencing data.

Tang S, Riva A.

BMC Bioinformatics. 2013 Apr 4;14:116. doi: 10.1186/1471-2105-14-116.


UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.

Burns PD, Li Y, Ma J, Borodovsky M.

Nucleic Acids Res. 2014 Feb;42(4):e25. doi: 10.1093/nar/gkt1141. Epub 2013 Nov 19.


CLASS: constrained transcript assembly of RNA-seq reads.

Song L, Florea L.

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.


OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.

Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C.

Nucleic Acids Res. 2013 May 1;41(10):5149-63. doi: 10.1093/nar/gkt216. Epub 2013 Apr 9.

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