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Items: 1 to 20 of 105

1.

An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data.

Okoniewski MJ, Yates T, Dibben S, Miller CJ.

Genome Biol. 2007;8(5):R79.

2.

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Yates T, Okoniewski MJ, Miller CJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D780-6. Epub 2007 Oct 11.

3.

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
4.

ggbio: an R package for extending the grammar of graphics for genomic data.

Yin T, Cook D, Lawrence M.

Genome Biol. 2012 Aug 31;13(8):R77. doi: 10.1186/gb-2012-13-8-r77.

5.

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.

Yu G, Wang LG, He QY.

Bioinformatics. 2015 Jul 15;31(14):2382-3. doi: 10.1093/bioinformatics/btv145. Epub 2015 Mar 11.

PMID:
25765347
6.

Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.

Wilson CL, Miller CJ.

Bioinformatics. 2005 Sep 15;21(18):3683-5. Epub 2005 Aug 2.

PMID:
16076888
7.

HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data.

Gu Z, Eils R, Schlesner M.

Bioinformatics. 2016 Aug 1;32(15):2372-4. doi: 10.1093/bioinformatics/btw161. Epub 2016 Mar 24.

PMID:
27153599
8.

puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.

Liu X, Gao Z, Zhang L, Rattray M.

BMC Bioinformatics. 2013 Feb 5;14:39. doi: 10.1186/1471-2105-14-39.

9.

GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs.

Risueño A, Fontanillo C, Dinger ME, De Las Rivas J.

BMC Bioinformatics. 2010 Apr 29;11:221. doi: 10.1186/1471-2105-11-221.

10.

plethy: management of whole body plethysmography data in R.

Bottomly D, Wilmot B, McWeeney SK.

BMC Bioinformatics. 2015 Apr 29;16:134. doi: 10.1186/s12859-015-0547-7.

11.

GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome.

Folkersen L, Diez D, Wheelock CE, Haeggström JZ, Goto S, Eriksson P, Gabrielsen A.

Bioinformatics. 2009 Aug 1;25(15):1978-9. doi: 10.1093/bioinformatics/btp279. Epub 2009 Apr 27.

12.

MADS+: discovery of differential splicing events from Affymetrix exon junction array data.

Shen S, Warzecha CC, Carstens RP, Xing Y.

Bioinformatics. 2010 Jan 15;26(2):268-9. doi: 10.1093/bioinformatics/btp643. Epub 2009 Nov 17.

13.

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.

Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W755-62. doi: 10.1093/nar/gkq405. Epub 2010 May 31.

14.

Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data.

Yu H, Wang F, Tu K, Xie L, Li YY, Li YX.

BMC Bioinformatics. 2007 Jun 11;8:194.

15.

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.

Gu Z, Eils R, Schlesner M.

Bioinformatics. 2016 Sep 15;32(18):2847-9. doi: 10.1093/bioinformatics/btw313. Epub 2016 May 20.

PMID:
27207943
16.

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.

Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B.

Bioinformatics. 2013 Mar 1;29(5):666-8. doi: 10.1093/bioinformatics/bts708. Epub 2013 Jan 6.

17.

EBImage--an R package for image processing with applications to cellular phenotypes.

Pau G, Fuchs F, Sklyar O, Boutros M, Huber W.

Bioinformatics. 2010 Apr 1;26(7):979-81. doi: 10.1093/bioinformatics/btq046.

18.

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.

Luo W, Brouwer C.

Bioinformatics. 2013 Jul 15;29(14):1830-1. doi: 10.1093/bioinformatics/btt285. Epub 2013 Jun 4.

19.

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.

20.

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.

Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M.

Bioinformatics. 2014 Jul 15;30(14):2076-8. doi: 10.1093/bioinformatics/btu168. Epub 2014 Mar 28.

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