• Info
  • Data files
  • Adjust data
    • Transpose matrix
    • Annotation
    • Truncate data
    • Impute data
    • Replica averaging
    • Filter data
    • Conditions
      • Total intensity normalisation
      • Total rank normalisation
      • Mean variance normalisation
      • z-transformation
      • Quantile normalisation
      • Total rank centering
      • Control gene normalisation
      • ComBat
      • VST/RLog2
      • DESEQ2
    • Genes
      • Virtual pool normalisation
      • Hybridisation normalisation
      • z-transformation
    • Data transformation
      • Log2 transformation
      • Log10 to Log2
      • Exp2
      • Ratio to intensity
    • Aritmetic operations
      • Change sign
    • Back-up data
      • Back-up
      • Restore
      • Delete
  • Data views
    • Heat map
    • Box plots
    • Scatter plots
      • X-Y plots
      • R-I plots
      • Quantile plots
      • 3D plots
      • Mosaic plots
    • Histograms
    • Correlation maps
    • Deviation plots
    • Dot chart
    • Profiles/1D graphs
  • Select groups
    • Define number of groups
    • Assign conditions to groups
    • Manage groups
    • Use other group labels
    • Find conditions
    • Manage selections
    • Save / Load groupings
  • T-test
    • Single class
    • Two class
    • Paired samples Two class
    • Multi class
  • ANOVA
  • Non parametric tests
    • Man-Witney,Wilcoxon,
      Kruskal-Wallace
      • Test principle
      • Single class (Man-Whitney)
      • Two class (Man-Whitney)
      • Paired samples (Wilcoxon)
      • Multi class (Kruskal-Wallace)
    • Kolmogorov-Smirnov
      • Test principle
      • Two class test
      • Multi class test
  • Template matching
  • SAM
    • Single-, Two-, Multi-class SAM
      • Single class SAM
      • 2-class unpaired
      • Multi class
    • Quantitative response / survival
      • Quantitative response
      • Survival
    • Analysis tree
      • Parameter
      • Delta table
      • Delta graph
      • SAM graph
      • Gene lists
      • Gene sub-matrices
      • Gene profiles
      • Centroid profiles
      • Heat maps
  • Survival analyses
    • Kaplan-Meier
      • Edit data
      • Export data
      • Basic statistics
      • Log rank test
    • Survival filter 1
    • Survival filter 2
    • Survival filter 3
    • Survival filter 4
    • Cox regression
      • Date clean-up
        • Categorize
        • Categorize by k-Means
        • Binarize
        • Categories to binary groups
        • Shift positive
        • Invert
      • Row operator
        • Fill
        • Concatenate rows
        • Date difference
        • Replace text
        • Statistics
      • Filter
      • Sort
      • Define
      • Run
      • Troubleshooting
      • Set-up
  • Clustering
    • Hiearchical
    • K-means clustering
      • Basic Idea
      • Parameter
      • Data views
      • Convergence plot
      • Silhouette
    • Non negative Matrix Factorization (NMF)
      • NMF with SUMO
    • Distances
      • Geometric
      • Correlationy
      • Binary
    • Linkage
  • PCA/t-SNE/UMAP
    • Mathematics
    • Parameter
    • Data views
      • Parameter
      • Eigen-values
      • Eigen-vector table
      • Eigen-vector graph
      • Eigen-vector / Factor graph
      • Eigen-vector / Observables graph
    • t-SNE
    • UMAP
  • Classification
    • LDA - Linear Discriminant Analysis
    • KNN - K Nearest Neighbours
    • CC - Closest Centroid
    • ANN - Artificial Neural Network
    • SVM - Support Vector Machines
    • RF - Random Forests
  • CO-LOocalisation Mapper
    • Mathematical / statistical concepts
      • - Hypergeometric distribution
      • - GSEA - KM-Statistics
      • - SEA - Chi2-statistics
    • COLOM
    • Data bases / files
      • GO-Terms
      • KEGG
      • Chromosomal bands
      • miRNA
      • MSig-DB
      • Wiki pathways
      • Reactome
  • Gene-Net Builder
    • Basic Idea
    • Evidence for a network
    • Net work builder
    • Interaction lists
    • Network viewer
  • Venn diagrams
    • Venn with SUMO
    • 1-8 groups
    • The diagrams
    • Customize graphs
    • p-Enrichement
    • Venn heatmaps
    • List-Venn
    • Preferences
  • Analysis tree
    • Text info
    • Data tables
    • p-Value graph
    • Volcano plot
    • Line graphs / charts
    • Gene profiles
    • Centroid profiles"
    • Heat maps
  • Scripts
    • Editor
  • Parallel processing
  • Log-tab sheet
  • Utilities
    • Statistic tests
      • t-test
      • U-test
      • Kolomogorov-Sminov
      • Fisher exact test
      • Grubbs test
      • 2x2 Cross tables
      • Neumann trend test
      • Correlation r => p
      • p => Correlation r
      • Mantel test
    • Co-epression networks
    • Methylation
      • Extract Quants from IDat
      • M/U impute missing intensity values
      • Pairwise color quantile normalization
      • M/U Intensities => M or Beta
      • M/U Intensities => Total intensity
      • Methylation-BMIQ-normalisation
      • bumphunter
    • NGS
      • Filter SAM
      • SAM=>population map
      • Annotate
      • BED tools
        • View
        • Features=>Bumps
        • Class tests
        • AnnotateClass tests
      • SAM tools
        • QC
      • Count statistics
    • Feature list=>Matrix
      • Multiple lists=>Matrix
      • >Key-value pairs=>Matrix
      • >Key-value pairs=>Expression Matrix
    • File utilities
      • XML => TSV
      • >JSON => TSV
    • Sequence logos
    • Color picker
    • File/table viewer
    • Blast wrapper
    • Random number generator
  • Tutorials / How tos
    • RT-PCR
  • Preferences

  • FAQ
  • History


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