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Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.
Proper citation: CRCView (RRID:SCR_007092) Copy
http://www.bioconductor.org/packages/release/bioc/html/ARRmNormalization.html
Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.
Proper citation: ARRmNormalization (RRID:SCR_001292) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/minfi.html
Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.
Proper citation: SWAN (RRID:SCR_003455) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/VariantAnnotation.html
Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes.
Proper citation: VariantAnnotation (RRID:SCR_000074) Copy
https://rdrr.io/bioc/yaqcaffy/
Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.
Proper citation: yaqcaffy (RRID:SCR_001295) Copy
http://www.bioconductor.org/packages/release/bioc/html/ITALICS.html
Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set.
Proper citation: ITALICS (RRID:SCR_001274) Copy
https://www.bioconductor.org/packages//2.12/bioc/html/dexus.html
Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.
Proper citation: DEXUS (RRID:SCR_001309) Copy
http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html
Software package for various databases of microRNA Targets.
Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy
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