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Items: 1 to 20 of 121

1.

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.

2.

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
3.

Estimating RNA-quality using GeneChip microarrays.

Fasold M, Binder H.

BMC Genomics. 2012 May 14;13:186. doi: 10.1186/1471-2164-13-186.

4.

Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues.

Popova T, Mennerich D, Weith A, Quast K.

BMC Genomics. 2008 Feb 25;9:91. doi: 10.1186/1471-2164-9-91.

5.

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
6.

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.

7.

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.

Turro E, Bochkina N, Hein AM, Richardson S.

BMC Bioinformatics. 2007 Nov 12;8:439.

8.

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
9.

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.

10.

A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R.

Gregory Alvord W, Roayaei JA, Quiñones OA, Schneider KT.

Brief Bioinform. 2007 Nov;8(6):415-31. Epub 2007 Sep 29.

PMID:
17906332
11.
12.

Transcript mapping with high-density oligonucleotide tiling arrays.

Huber W, Toedling J, Steinmetz LM.

Bioinformatics. 2006 Aug 15;22(16):1963-70. Epub 2006 Jun 20.

PMID:
16787969
13.

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Bolstad BM, Irizarry RA, Astrand M, Speed TP.

Bioinformatics. 2003 Jan 22;19(2):185-93.

PMID:
12538238
14.

Comparison of Affymetrix GeneChip expression measures.

Irizarry RA, Wu Z, Jaffee HA.

Bioinformatics. 2006 Apr 1;22(7):789-94. Epub 2006 Jan 12.

PMID:
16410320
15.

Contrast normalization of oligonucleotide arrays.

Astrand M.

J Comput Biol. 2003;10(1):95-102.

PMID:
12676053
16.

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.

17.

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays.

Hekstra D, Taussig AR, Magnasco M, Naef F.

Nucleic Acids Res. 2003 Apr 1;31(7):1962-8.

18.

RefPlus: an R package extending the RMA Algorithm.

Harbron C, Chang KM, South MC.

Bioinformatics. 2007 Sep 15;23(18):2493-4. Epub 2007 Jul 10.

PMID:
17623700
19.

Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model.

Sásik R, Calvo E, Corbeil J.

Bioinformatics. 2002 Dec;18(12):1633-40.

PMID:
12490448
20.

Codelink: an R package for analysis of GE healthcare gene expression bioarrays.

Diez D, Alvarez R, Dopazo A.

Bioinformatics. 2007 May 1;23(9):1168-9. Epub 2007 Mar 7.

PMID:
17344240

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