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Items: 1 to 20 of 174

1.

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.

PMID:
24813215
2.

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.

3.

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.

PMID:
24535097
4.

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.

5.

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.

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.

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.

8.

RNASeqGUI: a GUI for analysing RNA-Seq data.

Russo F, Angelini C.

Bioinformatics. 2014 Sep 1;30(17):2514-6. doi: 10.1093/bioinformatics/btu308. Epub 2014 May 7.

PMID:
24812338
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.

DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification.

Chiesa M, Colombo GI, Piacentini L.

Bioinformatics. 2018 Apr 15;34(8):1416-1418. doi: 10.1093/bioinformatics/btx795.

PMID:
29236969
11.

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods.

Quinn TP, Crowley TM, Richardson MF.

BMC Bioinformatics. 2018 Jul 18;19(1):274. doi: 10.1186/s12859-018-2261-8.

12.

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.

13.

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

Zhu LJ, Lawrence M, Gupta A, Pagès H, Kucukural A, Garber M, Wolfe SA.

BMC Genomics. 2017 May 15;18(1):379. doi: 10.1186/s12864-017-3746-y.

14.

ClassifyR: an R package for performance assessment of classification with applications to transcriptomics.

Strbenac D, Mann GJ, Ormerod JT, Yang JY.

Bioinformatics. 2015 Jun 1;31(11):1851-3. doi: 10.1093/bioinformatics/btv066. Epub 2015 Feb 1.

PMID:
25644269
15.

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.

16.

msa: an R package for multiple sequence alignment.

Bodenhofer U, Bonatesta E, Horejš-Kainrath C, Hochreiter S.

Bioinformatics. 2015 Dec 15;31(24):3997-9. doi: 10.1093/bioinformatics/btv494. Epub 2015 Aug 26.

PMID:
26315911
17.

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.

Del Carratore F, Jankevics A, Eisinga R, Heskes T, Hong F, Breitling R.

Bioinformatics. 2017 Sep 1;33(17):2774-2775. doi: 10.1093/bioinformatics/btx292.

18.

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data.

Ihnatova I, Budinska E.

BMC Bioinformatics. 2015 Oct 29;16:350. doi: 10.1186/s12859-015-0763-1.

19.

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components.

Marini F, Binder H.

BMC Bioinformatics. 2019 Jun 13;20(1):331. doi: 10.1186/s12859-019-2879-1.

20.

Network module-based model in the differential expression analysis for RNA-seq.

Lei M, Xu J, Huang LC, Wang L, Li J.

Bioinformatics. 2017 Sep 1;33(17):2699-2705. doi: 10.1093/bioinformatics/btx214.

PMID:
28407034

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