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About BRB-ArrayTools

Expression Data

  • Supported Data Types 
BRB ArrayTools supported data types
  • Affymetrix 3'-IVT arrays
  • Affymetrix genechip ST 1.0 arrays
  • Agilent single and dual channel arrays
  • Illumina expression arrays
  • GenePix data
  • mAdb archive data
  • GDS datasets from NCBI/GEO
  • Other data types through general importer
  • RNA-Seq count data processed through Galaxy web tools
  • Class comparison for differential expression
    • Univariate tests with the option of random variance model 
Volcano plot from class comparison for differential expression in BRB ArrayTools
  • Multivariate permutation tests
  • Significance Analysis of Microarrays (SAM)
  • Lassoed Principal Components
  • Class prediction
    • Compound covariate predictor; SVM; Bayesian compound covariate; KNN; DLDA; 
BRB ArrayTools class prediction output
  • Nearest centroid
  • Adaboost
  • PAM
  • Lasso logistic regression
  • Binary tree prediction
  • Clustering 
BRB ArrayTools cluster analysis and dynamic heatmap
  • Interactive heatmap viewer, Hierarchical clustering, Non-negative matrix factorization clustering
  • 2-D and 3-D interactive Scatter-plot
    • Phenotype average
    • Array vs. Array
  • Gene Set Enrichment Analysis with many gene sets 
BRB ArrayTools gene set enrichment analysis
  • BioCarta, KEGG, CGAP, Broad Institute - MSigDB, Gene Ontology, Protein domain, Transcription factor targets, MicroRNA targets, User defined gene lists
  • Visualization of Samples 
BRB ArrayTools visualization of samples
  • 3-D interactive plot
  • Survival Analysis 
BRB ArrayTools survival analysis
  • Survival gene sets analysis
  • Survival risk prediction analysis
  • KEGG Pathway Graphic Tool
    • The Gene color coding for KEGG human disease pathways utility tool displays a KEGG disease pathway graph with selected genes being color-coded by their expression values or fold changes.  
BRB ArrayTools KEGG pathway network plot

Methylation Data

  • Import and process Illumina methylation data 
Process Illumina methylation data in BRB-ArrayTools
  • Find frequently methylated region
  • Create a heatmap with methylation data

Copy Number Data

  • Analyze copy number data in BRB CGHTools
  • Specification of Gain and Loss Calls analysis
BRB CGHTools Frequency Plot
Analyze copy number data in BRB CGHTools

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