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Items: 1 to 20 of 132

1.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Erratum in: Nat Protoc. 2014 Oct;9(10):2513.

2.

Analysis of RNA-Seq Data Using TopHat and Cufflinks.

Ghosh S, Chan CK.

Methods Mol Biol. 2016;1374:339-61. doi: 10.1007/978-1-4939-3167-5_18.

PMID:
26519415
3.

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL.

Nat Protoc. 2016 Sep;11(9):1650-67. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11.

4.

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment.

Zhang Z, Huang S, Wang J, Zhang X, Pardo Manuel de Villena F, McMillan L, Wang W.

Bioinformatics. 2013 Jul 1;29(13):i291-9. doi: 10.1093/bioinformatics/btt216.

5.

Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures.

Pollier J, Rombauts S, Goossens A.

Methods Mol Biol. 2013;1011:305-15. doi: 10.1007/978-1-62703-414-2_24.

PMID:
23616006
6.

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.

7.

Quantitative transcriptome analysis using RNA-seq.

Külahoglu C, Bräutigam A.

Methods Mol Biol. 2014;1158:71-91. doi: 10.1007/978-1-4939-0700-7_5.

PMID:
24792045
8.

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Brooks MJ, Rajasimha HK, Roger JE, Swaroop A.

Mol Vis. 2011;17:3034-54. Epub 2011 Nov 23.

9.

Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.

Watanabe KA, Homayouni A, Tufano T, Lopez J, Ringler P, Rushton P, Shen QJ.

DNA Res. 2015 Oct;22(5):319-29. doi: 10.1093/dnares/dsv015. Epub 2015 Sep 3.

10.

A comparison of methods for differential expression analysis of RNA-seq data.

Soneson C, Delorenzi M.

BMC Bioinformatics. 2013 Mar 9;14:91. doi: 10.1186/1471-2105-14-91.

11.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

12.

Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.

13.

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.

14.

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF.

Bioinformatics. 2011 Oct 1;27(19):2633-40. doi: 10.1093/bioinformatics/btr458. Epub 2011 Aug 8.

15.

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 9;14:320. doi: 10.1186/1471-2105-14-320.

16.

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq.

Macaulay IC, Teng MJ, Haerty W, Kumar P, Ponting CP, Voet T.

Nat Protoc. 2016 Nov;11(11):2081-103. doi: 10.1038/nprot.2016.138. Epub 2016 Sep 29.

PMID:
27685099
17.

Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA.

Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R.

J Vis Exp. 2011 Oct 27;(56):e3340. doi: 10.3791/3340.

18.

RNA-Seq: a method for comprehensive transcriptome analysis.

Nagalakshmi U, Waern K, Snyder M.

Curr Protoc Mol Biol. 2010 Jan;Chapter 4:Unit 4.11.1-13. doi: 10.1002/0471142727.mb0411s89.

PMID:
20069539
19.

Computational analysis of bacterial RNA-Seq data.

McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B.

Nucleic Acids Res. 2013 Aug;41(14):e140. doi: 10.1093/nar/gkt444. Epub 2013 May 28.

20.

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.

Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X.

Genome Biol. 2015 Feb 11;16:30. doi: 10.1186/s13059-015-0596-2.

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