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Results: 1 to 20 of 91

1.

Using high-density DNA methylation arrays to profile copy number alterations.

Feber A, Guilhamon P, Lechner M, Fenton T, Wilson GA, Thirlwell C, Morris TJ, Flanagan AM, Teschendorff AE, Kelly JD, Beck S.

Genome Biol. 2014 Feb 3;15(2):R30. doi: 10.1186/gb-2014-15-2-r30.

PMID:
24490765
[PubMed - in process]
Free PMC Article
2.

ChAMP: 450k Chip Analysis Methylation Pipeline.

Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S.

Bioinformatics. 2014 Feb 1;30(3):428-30. doi: 10.1093/bioinformatics/btt684. Epub 2013 Dec 12.

PMID:
24336642
[PubMed - indexed for MEDLINE]
3.

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.

Ritchie ME, Carvalho BS, Hetrick KN, Tavaré S, Irizarry RA.

Bioinformatics. 2009 Oct 1;25(19):2621-3. doi: 10.1093/bioinformatics/btp470. Epub 2009 Aug 6.

PMID:
19661241
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.

Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28.

PMID:
24478339
[PubMed - indexed for MEDLINE]
5.

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringnér M.

BMC Bioinformatics. 2008 Oct 2;9:409. doi: 10.1186/1471-2105-9-409.

PMID:
18831757
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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 Jun 27. pii: S1046-2023(14)00230-8. doi: 10.1016/j.ymeth.2014.06.008. [Epub ahead of print]

PMID:
24979058
[PubMed - as supplied by publisher]
7.

OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data.

Hu Y, Yan C, Hsu CH, Chen QR, Niu K, Komatsoulis GA, Meerzaman D.

Cancer Inform. 2014 Jan 16;13:13-20. doi: 10.4137/CIN.S13495. eCollection 2014.

PMID:
24526832
[PubMed]
Free PMC Article
8.

ADaCGH2: parallelized analysis of (big) CNA data.

Diaz-Uriarte R.

Bioinformatics. 2014 Jun 15;30(12):1759-61. doi: 10.1093/bioinformatics/btu099. Epub 2014 Feb 14.

PMID:
24532724
[PubMed - in process]
9.

Marmal-aid--a database for Infinium HumanMethylation450.

Lowe R, Rakyan VK.

BMC Bioinformatics. 2013 Dec 12;14:359. doi: 10.1186/1471-2105-14-359.

PMID:
24330312
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Akman K, Haaf T, Gravina S, Vijg J, Tresch A.

Bioinformatics. 2014 Jul 1;30(13):1933-4. doi: 10.1093/bioinformatics/btu142. Epub 2014 Mar 10.

PMID:
24618468
[PubMed - in process]
11.

SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.

Maksimovic J, Gordon L, Oshlack A.

Genome Biol. 2012 Jun 15;13(6):R44. doi: 10.1186/gb-2012-13-6-r44.

PMID:
22703947
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data.

Nguyen HT, Merriman TR, Black MA.

Front Genet. 2014 Aug 1;5:248. doi: 10.3389/fgene.2014.00248. eCollection 2014.

PMID:
25136349
[PubMed]
Free PMC Article
13.

VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets.

Morganella S, Ceccarelli M.

Bioinformatics. 2012 Oct 1;28(19):2512-4. Epub 2012 Jul 18.

PMID:
22815357
[PubMed - indexed for MEDLINE]
Free Article
14.

Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations.

Wong G, Leckie C, Gorringe KL, Haviv I, Campbell IG, Kowalczyk A.

Bioinformatics. 2010 Apr 15;26(8):1007-14. doi: 10.1093/bioinformatics/btq088. Epub 2010 Feb 25.

PMID:
20189937
[PubMed - indexed for MEDLINE]
Free Article
15.

The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome.

Przybytkowski E, Ferrario C, Basik M.

BMC Med Genomics. 2011 Jan 27;4:16. doi: 10.1186/1755-8794-4-16.

PMID:
21272361
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.

Ostrovnaya I, Seshan VE, Olshen AB, Begg CB.

Bioinformatics. 2011 Jun 15;27(12):1698-9. doi: 10.1093/bioinformatics/btr267. Epub 2011 May 5.

PMID:
21546399
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer.

Kloth JN, Oosting J, van Wezel T, Szuhai K, Knijnenburg J, Gorter A, Kenter GG, Fleuren GJ, Jordanova ES.

BMC Genomics. 2007 Feb 20;8:53.

PMID:
17311676
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells.

Liu Z, Li A, Schulz V, Chen M, Tuck D.

PLoS One. 2010 Jun 1;5(6):e10909. doi: 10.1371/journal.pone.0010909.

PMID:
20532221
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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
20.

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.

Yu G, Zhang B, Bova GS, Xu J, Shih IeM, Wang Y.

Bioinformatics. 2011 Jun 1;27(11):1473-80. doi: 10.1093/bioinformatics/btr183. Epub 2011 Apr 15.

PMID:
21498400
[PubMed - indexed for MEDLINE]
Free PMC Article

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