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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.


compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.

Soneson C.

Bioinformatics. 2014 Sep 1;30(17):2517-8. doi: 10.1093/bioinformatics/btu324. Epub 2014 May 9.


ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.

Huntley MA, Larson JL, Chaivorapol C, Becker G, Lawrence M, Hackney JA, Kaminker JS.

Bioinformatics. 2013 Dec 15;29(24):3220-1. doi: 10.1093/bioinformatics/btt551. Epub 2013 Sep 29.


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.


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.


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.


SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.

Wang X, Cairns MJ.

Bioinformatics. 2014 Jun 15;30(12):1777-9. doi: 10.1093/bioinformatics/btu090. Epub 2014 Feb 17.


AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.

Fasold M, Binder H.

Bioinformatics. 2013 Jan 1;29(1):129-31. doi: 10.1093/bioinformatics/bts629. Epub 2012 Oct 24.


RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.

Li Y, Zhao DY, Greenblatt JF, Zhang Z.

Nucleic Acids Res. 2013 Apr;41(8):e94. doi: 10.1093/nar/gkt142. Epub 2013 Feb 28.


A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.

Meng J, Lu Z, Liu H, Zhang L, Zhang S, Chen Y, Rao MK, Huang Y.

Methods. 2014 Oct 1;69(3):274-81. doi: 10.1016/j.ymeth.2014.06.008. Epub 2014 Jun 27.


HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.

Wang X, Terfve C, Rose JC, Markowetz F.

Bioinformatics. 2011 Mar 15;27(6):879-80. doi: 10.1093/bioinformatics/btr028. Epub 2011 Jan 22.


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.


A new approach to bias correction in RNA-Seq.

Jones DC, Ruzzo WL, Peng X, Katze MG.

Bioinformatics. 2012 Apr 1;28(7):921-8. doi: 10.1093/bioinformatics/bts055. Epub 2012 Jan 28.


spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

Vitting-Seerup K, Porse BT, Sandelin A, Waage J.

BMC Bioinformatics. 2014 Mar 23;15:81. doi: 10.1186/1471-2105-15-81.


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.


Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.

Toedling J, Ciaudo C, Voinnet O, Heard E, Barillot E.

Bioinformatics. 2010 Nov 15;26(22):2902-3. doi: 10.1093/bioinformatics/btq531. Epub 2010 Sep 21.


Importing ArrayExpress datasets into R/Bioconductor.

Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.

Bioinformatics. 2009 Aug 15;25(16):2092-4. doi: 10.1093/bioinformatics/btp354. Epub 2009 Jun 8.


RSeQC: quality control of RNA-seq experiments.

Wang L, Wang S, Li W.

Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27.


BayesPeak--an R package for analysing ChIP-seq data.

Cairns J, Spyrou C, Stark R, Smith ML, Lynch AG, Tavaré S.

Bioinformatics. 2011 Mar 1;27(5):713-4. doi: 10.1093/bioinformatics/btq685. Epub 2011 Jan 17.


Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.

Yu D, Huber W, Vitek O.

Bioinformatics. 2013 May 15;29(10):1275-82. doi: 10.1093/bioinformatics/btt143. Epub 2013 Apr 14.

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