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Finding recurrent copy number alterations preserving within-sample homogeneity.
Morganella S, Pagnotta SM, Ceccarelli M. Morganella S, et al. Bioinformatics. 2011 Nov 1;27(21):2949-56. doi: 10.1093/bioinformatics/btr488. Epub 2011 Aug 25. Bioinformatics. 2011. PMID: 21873327
In addition, we perform an accurate comparison by using two real aCGH datasets and a carefully planned simulation study. AVAILABILITY: GAIA has been implemented as R/Bioconductor package. It can be downloaded from the following page http://bioinformatics.biogem.it/download …
In addition, we perform an accurate comparison by using two real aCGH datasets and a carefully planned simulation study. AVAILABILITY: GA …
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.
Silva TC, Colaprico A, Olsen C, D'Angelo F, Bontempi G, Ceccarelli M, Noushmehr H. Silva TC, et al. F1000Res. 2016 Jun 29;5:1542. doi: 10.12688/f1000research.8923.2. eCollection 2016. F1000Res. 2016. PMID: 28232861 Free PMC article.
This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox, TCGAbiolinks....
This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET …