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Welcome to comicsArt
Data selection
Pre-processing
Sample Correlation
PCA
Significance Analysis
Heatmap
Single Gene Visualisations
Enrichment Analysis
User Help
Sidebar
Here you can select parameters which are important for your analysis.
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Main Panel
Tour around cOmicsArt
Take me to the Analysis Start
Data Selection
File Input
Precompiled
Metadata
Testdata
Omic Type that is uploaded
Transcriptomics
Lipidomics
Metabolomics
Upload
Download an example Excel Workbook to prepare data upload
Data matrix
Download example data
Browse...
Sample annotation
Download example data
Browse...
Entities annotation
Download example data
Browse...
Inspect data
Upload new data
Omic Type that is uploaded
Transcriptomics
Lipidomics
Metabolomics
Load precompiled data
(saved in this procedure or type SummarizedExperiment)
Download example data
Browse...
Upload new data
Omic Type that is uploaded
Transcriptomics
Lipidomics
Metabolomics
Upload data matrix
(rows entities, cols samples)
Download example data (Transcriptomics, human)
Browse...
Upload your Meta Data Sheet
(currently replaces sample annotation)
Simply upload your Metadata Sheet!
Upload entities annotation matrix
(rows must be entities)
Download example data
Browse...
Upload new data
Omic Type that is uploaded
Transcriptomics
Upload test data
(show/hide) Further entitie Annotation options
[optional] Select Data
Go to Preprocessing
Row selection - biochemical entities
Sample selection
Save file input to upload later
Start the Journey
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Data Pre-processing
Pre-Processing Procedures
No pre-processing
Omic-specific filtering of low abundance
DESeq2 pre-processing (including variance stabilising transformation)
centering to 0 and scaling
scaling values to be within 0 and 1
log10
log2
Pareto scaling (mean-centered and scaled by the square root of the standard deviation)
natural logarithm
Get Pre-Processing
Raw Data
Pre-processed Data
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
Sample Correlation
Sample Correlation
Choose the correlation method
pearson
kendall
spearman
Get Sample Correlation
Refresh
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
PCA
Explorative Analysis
Scale data to unit variance?
Yes
No
Get PCA
PC for x-Axis
PC1
PC2
PC3
PC4
PC for y-Axis
PC1
PC2
PC3
PC4
Plot Loadings on top? (currently top 5)
Yes
No
Note: if you would like to change the annotation of the indicated loading vectors please select an option the the tab Loadings
Refresh
PCA_plot
PCA_Loadings
PCA_Loadings_matrix
Scree_Plot
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
Top k positive Loadings
Top k negative Loadings
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
absolute Loading threshold to filter entities with low impact
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Significance Analysis
Significance level
Multiple testing correction
None
Bonferroni
Benjamini-Hochberg
Benjamini Yekutieli
Holm
Hommel
Hochberg
FDR
Get Significance Analysis
Refresh UI
Result Visualization
Visualization Choices
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
Heatmap
Select Entities to show
all
Select based on Annotation
Top K
Further row selection (LFC based)
Order based on
LogFoldChange
absolute LogFoldChange
LogFoldChange and Significant
absolute LogFoldChange and Significant
Choose number of top entities to show (order based on p-val (LFC) or rowCount)
adj. p-value threshold
Further row selection (annotation based)
Get Heatmap
Aesthetics
Row Clustering?
Column Clustering?
row-wise scaling?
Refresh
Threshold upon which explicit labels are shown
Save genes shown in Heatmap for OA within Enrichment Analysis tab
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
Single Gene Visualisations
Get Single Gene Visualisation
Refresh
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
Enrichment Analysis
Choose type of Analysis
GeneSetEnrichment
OverRepresentation_Analysis
Test correction
None
Bonferroni
Benjamini-Hochberg
Benjamini Yekutieli
Holm
Hommel
Hochberg
FDR
Get Enrichment Analysis
Refresh UI
Hallmarks
C1
C2
CGP
CP
BIOCARTA
KEGG
PID
REACTOME
WIKIPATHWAYS
C3
MIRDB
MIR_Legacy
GTRD
TFT_Legacy
C4
CGN
CM
C5
GO
GO_BP
GO_CC
GO_MF
HPO
C6
C7
IMMUNESIGDB
VAX
C8
KeggPathwayOutput
Hallmarks Enrichment
Hallmarks Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C1 Enrichment
C1 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C2 Enrichment
C2 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
CGP Enrichment
CGP Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
CP Enrichment
CP Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
BIOCARTA Enrichment
BIOCARTA Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
KEGG Enrichment
KEGG Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
PID Enrichment
PID Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
REACTOME Enrichment
REACTOME Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
WIKIPATHWAYS Enrichment
WIKIPATHWAYS Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C3 Enrichment
C3 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
MIRDB Enrichment
MIRDB Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
MIR_Legacy Enrichment
MIR_Legacy Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
GTRD Enrichment
GTRD Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
TFT_Legacy Enrichment
TFT_Legacy Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C4 Enrichment
C4 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
CGN Enrichment
CGN Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
CM Enrichment
CM Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C5 Enrichment
C5 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
GO Enrichment
GO Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
GO_BP Enrichment
GO_BP Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
GO_CC Enrichment
GO_CC Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
GO_MF Enrichment
GO_MF Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
HPO Enrichment
HPO Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C6 Enrichment
C6 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C7 Enrichment
C7 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
IMMUNESIGDB Enrichment
IMMUNESIGDB Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
VAX Enrichment
VAX Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
C8 Enrichment
C8 Enrichment Table
Send only to Report
Get underlying R code and data
Save plot
File Type:
.png
.tiff
.pdf
Notes:
Here you can find a Markdown Cheat Sheet
Please do not use heading mardkown syntax - this will interfere with the reports hierachy
Specificy on the left which pathway (all sig. enriched) to display in picture-format
Show overlay on Pathway
Specifiy the what the colored overlay should indicate
LFC
presence
Adjust Width
Adjust Height
AuthorBirthdays
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Brought to you by Lea Seep & Paul Jonas Jost
It is Lea's birthday today :)
It is Paul's birthday today :)