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Items: 1 to 20 of 264

1.

BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.

Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y, Liang H.

BMC Genomics. 2012;13 Suppl 8:S9. doi: 10.1186/1471-2164-13-S8-S9. Epub 2012 Dec 17.

2.

BM-map: Bayesian mapping of multireads for next-generation sequencing data.

Ji Y, Xu Y, Zhang Q, Tsui KW, Yuan Y, Norris C Jr, Liang S, Liang H.

Biometrics. 2011 Dec;67(4):1215-24. doi: 10.1111/j.1541-0420.2011.01605.x. Epub 2011 Apr 22.

3.

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.

Xu G, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.

Source Code Biol Med. 2011 Jan 13;6(1):2. doi: 10.1186/1751-0473-6-2.

4.

Grape RNA-Seq analysis pipeline environment.

Knowles DG, Röder M, Merkel A, Guigó R.

Bioinformatics. 2013 Mar 1;29(5):614-21. doi: 10.1093/bioinformatics/btt016. Epub 2013 Jan 17.

5.

UMARS: Un-MAppable Reads Solution.

Li SC, Chan WC, Lai CH, Tsai KW, Hsu CN, Jou YS, Chen HC, Chen CH, Lin WC.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S9. doi: 10.1186/1471-2105-12-S1-S9.

6.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

7.

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:S2. doi: 10.1186/1471-2105-12-S5-S2. Epub 2011 Jul 27.

8.

S-MART, a software toolbox to aid RNA-Seq data analysis.

Zytnicki M, Quesneville H.

PLoS One. 2011;6(10):e25988. doi: 10.1371/journal.pone.0025988. Epub 2011 Oct 6.

9.

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics.

Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7. doi: 10.1093/nar/gks540. Epub 2012 Jun 8.

10.

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L.

BMC Genomics. 2014 Mar 5;15:176. doi: 10.1186/1471-2164-15-176.

11.

OSA: a fast and accurate alignment tool for RNA-Seq.

Hu J, Ge H, Newman M, Liu K.

Bioinformatics. 2012 Jul 15;28(14):1933-4. doi: 10.1093/bioinformatics/bts294. Epub 2012 May 15.

12.

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.

13.

ZOOM Lite: next-generation sequencing data mapping and visualization software.

Zhang Z, Lin H, Ma B.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W743-8. doi: 10.1093/nar/gkq538. Epub 2010 Jun 8.

14.

Oculus: faster sequence alignment by streaming read compression.

Veeneman BA, Iyer MK, Chinnaiyan AM.

BMC Bioinformatics. 2012 Nov 13;13:297. doi: 10.1186/1471-2105-13-297.

15.

QualitySNPng: a user-friendly SNP detection and visualization tool.

Nijveen H, van Kaauwen M, Esselink DG, Hoegen B, Vosman B.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W587-90. doi: 10.1093/nar/gkt333. Epub 2013 Apr 30.

16.

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

Liao Y, Smyth GK, Shi W.

Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13.

17.

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. doi: 10.1002/0471250953.bi1106s32.

PMID:
21154708
18.

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Li B, Dewey CN.

BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323.

19.

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data.

Ma X, Zhang X.

BMC Bioinformatics. 2013 Jul 10;14:220. doi: 10.1186/1471-2105-14-220.

20.

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.

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