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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.


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.


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.


DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions.

Klambauer G, Unterthiner T, Hochreiter S.

Nucleic Acids Res. 2013 Nov;41(21):e198. doi: 10.1093/nar/gkt834.


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.


Power analysis and sample size estimation for RNA-Seq differential expression.

Ching T, Huang S, Garmire LX.

RNA. 2014 Nov;20(11):1684-96. doi: 10.1261/rna.046011.114.


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.


Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads.

Chen HI, Liu Y, Zou Y, Lai Z, Sarkar D, Huang Y, Chen Y.

BMC Genomics. 2015;16 Suppl 7:S14. doi: 10.1186/1471-2164-16-S7-S14.


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.


LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data.

Lin B, Zhang LF, Chen X.

BMC Genomics. 2014;15 Suppl 10:S7. doi: 10.1186/1471-2164-15-S10-S7.


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.


Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.

McCarthy DJ, Chen Y, Smyth GK.

Nucleic Acids Res. 2012 May;40(10):4288-97. doi: 10.1093/nar/gks042.


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.


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.


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.


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.


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.


Differential meta-analysis of RNA-seq data from multiple studies.

Rau A, Marot G, Jaffrézic F.

BMC Bioinformatics. 2014 Mar 29;15:91. doi: 10.1186/1471-2105-15-91.


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.


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.

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