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
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Data views
Heat map
Box plots
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R-I plots
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3D plots
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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
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ANOVA
Non parametric tests
Man-Witney,Wilcoxon,
Kruskal-Wallace
Test principle
Single class (Man-Whitney)
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Kolmogorov-Smirnov
Test principle
Two class test
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Template matching
SAM
Single-, Two-, Multi-class SAM
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2-class unpaired
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Quantitative response / survival
Quantitative response
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Analysis tree
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Gene lists
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Heat maps
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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
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Date difference
Replace text
Statistics
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Clustering
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Basic Idea
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Convergence plot
Silhouette
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NMF with
SUMO
Distances
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Linkage
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Mathematics
Parameter
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Parameter
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Eigen-vector table
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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 - Chi
2
-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
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