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Results: 1 to 20 of 116

1.

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
2.

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
3.

TCC: an R package for comparing tag count data with robust normalization strategies.

Sun J, Nishiyama T, Shimizu K, Kadota K.

BMC Bioinformatics. 2013 Jul 9;14:219. doi: 10.1186/1471-2105-14-219.

PMID:
23837715
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
5.

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
6.

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
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.

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor.

Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD.

Nat Protoc. 2013 Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099. Epub 2013 Aug 22.

PMID:
23975260
[PubMed - indexed for MEDLINE]
9.

SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples.

Kimes PK, Cabanski CR, Wilkerson MD, Zhao N, Johnson AR, Perou CM, Makowski L, Maher CA, Liu Y, Marron JS, Hayes DN.

Nucleic Acids Res. 2014;42(14):e113. doi: 10.1093/nar/gku521. Epub 2014 Jul 16.

PMID:
25030904
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23557086
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression.

George NI, Chang CW.

BMC Bioinformatics. 2014 Mar 31;15:92. doi: 10.1186/1471-2105-15-92.

PMID:
24685233
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A powerful and flexible approach to the analysis of RNA sequence count data.

Zhou YH, Xia K, Wright FA.

Bioinformatics. 2011 Oct 1;27(19):2672-8. doi: 10.1093/bioinformatics/btr449. Epub 2011 Aug 2.

PMID:
21810900
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

easyRNASeq: a bioconductor package for processing RNA-Seq data.

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM.

Bioinformatics. 2012 Oct 1;28(19):2532-3. Epub 2012 Jul 30.

PMID:
22847932
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering.

Sîrbu A, Kerr G, Crane M, Ruskin HJ.

PLoS One. 2012;7(12):e50986. doi: 10.1371/journal.pone.0050986. Epub 2012 Dec 10.

PMID:
23251411
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
21816040
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
22684630
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
23449093
[PubMed - indexed for MEDLINE]
Free Article
18.

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Wang L, Feng Z, Wang X, Wang X, Zhang X.

Bioinformatics. 2010 Jan 1;26(1):136-8. doi: 10.1093/bioinformatics/btp612. Epub 2009 Oct 24.

PMID:
19855105
[PubMed - indexed for MEDLINE]
Free Article
19.

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.

PMID:
23497356
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

Nueda MJ, Tarazona S, Conesa A.

Bioinformatics. 2014 Sep 15;30(18):2598-602. doi: 10.1093/bioinformatics/btu333. Epub 2014 Jun 3.

PMID:
24894503
[PubMed - indexed for MEDLINE]
Free PMC Article

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