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Items: 1 to 20 of 213

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.

2.

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.

Johnson BK, Scholz MB, Teal TK, Abramovitch RB.

BMC Bioinformatics. 2016 Feb 4;17:66. doi: 10.1186/s12859-016-0923-y.

3.

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.

4.

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.

Xu G, Strong MJ, Lacey MR, Baribault C, Flemington EK, Taylor CM.

PLoS One. 2014 Feb 25;9(2):e89445. doi: 10.1371/journal.pone.0089445. eCollection 2014.

5.

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud.

Griffith M, Walker JR, Spies NC, Ainscough BJ, Griffith OL.

PLoS Comput Biol. 2015 Aug 6;11(8):e1004393. doi: 10.1371/journal.pcbi.1004393. eCollection 2015 Aug.

6.

Polyester: simulating RNA-seq datasets with differential transcript expression.

Frazee AC, Jaffe AE, Langmead B, Leek JT.

Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28.

7.

RNA-Seq Analysis Pipeline Based on Oshell Environment.

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

IEEE/ACM Trans Comput Biol Bioinform. 2014 Sep-Oct;11(5):973-8. doi: 10.1109/TCBB.2014.2321156.

PMID:
26356868
8.

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.

9.

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.

10.

Accurate inference of isoforms from multiple sample RNA-Seq data.

Tasnim M, Ma S, Yang EW, Jiang T, Li W.

BMC Genomics. 2015;16 Suppl 2:S15. doi: 10.1186/1471-2164-16-S2-S15. Epub 2015 Jan 21.

11.

READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data.

Förstner KU, Vogel J, Sharma CM.

Bioinformatics. 2014 Dec 1;30(23):3421-3. doi: 10.1093/bioinformatics/btu533. Epub 2014 Aug 13.

PMID:
25123900
12.

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
13.

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.

14.

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
15.

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies.

Chu C, Fang Z, Hua X, Yang Y, Chen E, Cowley AW Jr, Liang M, Liu P, Lu Y.

BMC Genomics. 2015 Jun 13;16:455. doi: 10.1186/s12864-015-1676-0.

16.

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.

17.

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
18.

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
19.

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.

20.

Experimental Design and Power Calculation for RNA-seq Experiments.

Wu Z, Wu H.

Methods Mol Biol. 2016;1418:379-90. doi: 10.1007/978-1-4939-3578-9_18.

PMID:
27008024

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