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Results: 1 to 20 of 173

1.

SpeCond: a method to detect condition-specific gene expression.

Cavalli FM, Bourgon R, Vaquerizas JM, Luscombe NM.

Genome Biol. 2011 Oct 18;12(10):R101. doi: 10.1186/gb-2011-12-10-r101. Erratum in: Genome Biol. 2011;12(12):413. Huber, Wolfgang [removed].

PMID:
22008066
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.

Castro MA, Wang X, Fletcher MN, Meyer KB, Markowetz F.

Genome Biol. 2012 Apr 24;13(4):R29. doi: 10.1186/gb-2012-13-4-r29.

PMID:
22531049
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19505942
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

metahdep: meta-analysis of hierarchically dependent gene expression studies.

Stevens JR, Nicholas G.

Bioinformatics. 2009 Oct 1;25(19):2619-20. doi: 10.1093/bioinformatics/btp468. Epub 2009 Jul 30.

PMID:
19648140
[PubMed - indexed for MEDLINE]
Free Article
5.

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.

PMID:
20861030
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.

Carey VJ, Davis AR, Lawrence MF, Gentleman R, Raby BA.

Bioinformatics. 2009 Jun 1;25(11):1447-8. doi: 10.1093/bioinformatics/btp169. Epub 2009 Apr 5.

PMID:
19349284
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Normal uniform mixture differential gene expression detection for cDNA microarrays.

Dean N, Raftery AE.

BMC Bioinformatics. 2005 Jul 12;6:173.

PMID:
16011807
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

FABIA: factor analysis for bicluster acquisition.

Hochreiter S, Bodenhofer U, Heusel M, Mayr A, Mitterecker A, Kasim A, Khamiakova T, Van Sanden S, Lin D, Talloen W, Bijnens L, Göhlmann HW, Shkedy Z, Clevert DA.

Bioinformatics. 2010 Jun 15;26(12):1520-7. doi: 10.1093/bioinformatics/btq227. Epub 2010 Apr 23.

PMID:
20418340
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).

Aryee MJ, Gutiérrez-Pabello JA, Kramnik I, Maiti T, Quackenbush J.

BMC Bioinformatics. 2009 Dec 10;10:409. doi: 10.1186/1471-2105-10-409.

PMID:
20003283
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

GeneExpressionSignature: an R package for discovering functional connections using gene expression signatures.

Li F, Cao Y, Han L, Cui X, Xie D, Wang S, Bo X.

OMICS. 2013 Feb;17(2):116-8. doi: 10.1089/omi.2012.0087.

PMID:
23374109
[PubMed - indexed for MEDLINE]
11.

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data.

Zhao H, Engelen K, De Moor B, Marchal K.

Bioinformatics. 2007 Jul 1;23(13):1700-1. Epub 2007 May 7.

PMID:
17485432
[PubMed - indexed for MEDLINE]
Free Article
12.

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.

Sanges R, Cordero F, Calogero RA.

Bioinformatics. 2007 Dec 15;23(24):3406-8. Epub 2007 Sep 17.

PMID:
17875544
[PubMed - indexed for MEDLINE]
Free Article
13.

Software packages for quantitative microarray-based gene expression analysis.

Dresen IM, Hüsing J, Kruse E, Boes T, Jöckel KH.

Curr Pharm Biotechnol. 2003 Dec;4(6):417-37. Review.

PMID:
14683435
[PubMed - indexed for MEDLINE]
14.

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Robinson MD, McCarthy DJ, Smyth GK.

Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11.

PMID:
19910308
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Query large scale microarray compendium datasets using a model-based bayesian approach with variable selection.

Hu M, Qin ZS.

PLoS One. 2009;4(2):e4495. doi: 10.1371/journal.pone.0004495. Epub 2009 Feb 13.

PMID:
19214232
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
24078713
[PubMed - indexed for MEDLINE]
17.

WebArray: an online platform for microarray data analysis.

Xia X, McClelland M, Wang Y.

BMC Bioinformatics. 2005 Dec 21;6:306.

PMID:
16371165
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Implementation of a gene expression index calculation method based on the PDNN model.

Nielsen HB, Gautier L, Knudsen S.

Bioinformatics. 2005 Mar 1;21(5):687-8. Epub 2004 Oct 27.

PMID:
15509605
[PubMed - indexed for MEDLINE]
Free Article
19.

The effects of probe binding affinity differences on gene expression measurements and how to deal with them.

Dannemann M, Lorenc A, Hellmann I, Khaitovich P, Lachmann M.

Bioinformatics. 2009 Nov 1;25(21):2772-9. doi: 10.1093/bioinformatics/btp492. Epub 2009 Aug 18.

PMID:
19689957
[PubMed - indexed for MEDLINE]
Free Article
20.

Novel software package for cross-platform transcriptome analysis (CPTRA).

Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. doi: 10.1186/1471-2105-10-S11-S16.

PMID:
19811681
[PubMed - indexed for MEDLINE]
Free PMC Article

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