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Results: 1 to 20 of 163

1.

Cloud-scale RNA-sequencing differential expression analysis with Myrna.

Langmead B, Hansen KD, Leek JT.

Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.

PMID:
20701754
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A pipeline for RNA-seq data processing and quality assessment.

Goncalves A, Tikhonov A, Brazma A, Kapushesky M.

Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.

PMID:
21233166
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.

Bi Y, Davuluri RV.

BMC Bioinformatics. 2013 Aug 27;14:262. doi: 10.1186/1471-2105-14-262.

PMID:
23981227
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.

Esnaola M, Puig P, Gonzalez D, Castelo R, Gonzalez JR.

BMC Bioinformatics. 2013 Aug 21;14:254. doi: 10.1186/1471-2105-14-254.

PMID:
23965047
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

RNA-Seq: revelation of the messengers.

Van Verk MC, Hickman R, Pieterse CM, Van Wees SC.

Trends Plant Sci. 2013 Apr;18(4):175-9. doi: 10.1016/j.tplants.2013.02.001. Epub 2013 Mar 5.

PMID:
23481128
[PubMed - indexed for MEDLINE]
6.

How to analyze gene expression using RNA-sequencing data.

Ramsköld D, Kavak E, Sandberg R.

Methods Mol Biol. 2012;802:259-74. doi: 10.1007/978-1-61779-400-1_17.

PMID:
22130886
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
23329413
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

From RNA-seq reads to differential expression results.

Oshlack A, Robinson MD, Young MD.

Genome Biol. 2010;11(12):220. doi: 10.1186/gb-2010-11-12-220. Epub 2010 Dec 22. Review.

PMID:
21176179
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Streaming fragment assignment for real-time analysis of sequencing experiments.

Roberts A, Pachter L.

Nat Methods. 2013 Jan;10(1):71-3. doi: 10.1038/nmeth.2251. Epub 2012 Nov 18.

PMID:
23160280
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.

Frazee AC, Langmead B, Leek JT.

BMC Bioinformatics. 2011 Nov 16;12:449. doi: 10.1186/1471-2105-12-449.

PMID:
22087737
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A.

BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

PMID:
24330401
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses.

Jourdren L, Bernard M, Dillies MA, Le Crom S.

Bioinformatics. 2012 Jun 1;28(11):1542-3. doi: 10.1093/bioinformatics/bts165. Epub 2012 Apr 5.

PMID:
22492314
[PubMed - indexed for MEDLINE]
Free Article
13.

RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A.

Bioinformatics. 2012 Apr 15;28(8):1184-5. doi: 10.1093/bioinformatics/bts084. Epub 2012 Feb 17.

PMID:
22345621
[PubMed - indexed for MEDLINE]
Free Article
14.

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.

Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E.

Bioinformatics. 2011 Dec 15;27(24):3333-40. doi: 10.1093/bioinformatics/btr570. Epub 2011 Oct 12.

PMID:
21994224
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.

Friedman BA, Maniatis T.

Genome Biol. 2011 Jul 28;12(7):R69. doi: 10.1186/gb-2011-12-7-r69.

PMID:
21797991
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Identifying differentially expressed transcripts from RNA-seq data with biological variation.

Glaus P, Honkela A, Rattray M.

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.

PMID:
22563066
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data.

Larsen PE, Collart FR.

BMC Res Notes. 2012 Jun 7;5:275. doi: 10.1186/1756-0500-5-275.

PMID:
22676709
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.

Mittal VK, McDonald JF.

Nucleic Acids Res. 2012 May;40(9):e67. doi: 10.1093/nar/gks047. Epub 2012 Jan 28.

PMID:
22287631
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Differential expression analysis for sequence count data.

Anders S, Huber W.

Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub 2010 Oct 27.

PMID:
20979621
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

Łabaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP.

Bioinformatics. 2011 Jul 1;27(13):i383-91. doi: 10.1093/bioinformatics/btr247.

PMID:
21685096
[PubMed - indexed for MEDLINE]
Free PMC Article

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