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Import TCGA Datasets
Full tumor name list
Import
Full tumor name list
Import Data
Select file:
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Add samples
Added files:
Import
Download Variants
Upload Musica
Upload Musica Result or Object
Musica Result
Musica Object
Upload Musica Result or Object:
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Upload
Download Variants
Create Musica Object
Settings
Check Reference Chromosomes
Check Reference Bases
Convert DBS
Standardize Indels
Create Musica Object
Download Musica Object
Create Tables
Select Count Table
SBS96
SBS192 - Transcript_Strand
SBS192 - Replication_Strand
DBS
Indel
Reference genome:
hg38
hg19
mm9
mm10
Add Sample Annotations
Upload Sample Annotations
Annotations file:
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Header
Delimiter
comma
tab
space
pipe
semicolon
custom
Delimiter
Add Annotation
Discover Signatures and Exposures
Custon Table Name
Number of signatures
Method
Latent Dirichlet Allocation (lda)
Negative Matrix Factorization (nmf)
Number of random starts
Discover Signatures
Predict Signature Exposures
Algorithm
Latent Dirichlet Allocation (lda)
decompTumor2Sig
deconstructSigs
Reference genome:
hg38
hg19
mm9
mm10
Predict Signature Exposures
Compare Signatures
Threshold
Similarity Metric
Cosine
Jensen-Shannon Divergence (jsd)
Compare Results
Differential Analysis
Method
Wilcoxon Rank Sum Test
Kruskal-Wallis Rank Sum Test
Negative Binomial Regression
Run Differential Analysis
Download
Visualize Signatures & Exposures
Signatures
Exposures
Settings
Rename Signatures
Text Size
Facet Size
Legend
X-axis Label
Same Y-axis Scale
Plotly
Make Plot
General Settings
Plot Type
Bar Plot
Box Plot
Violin Plot
Scatter Plot
Proportional
Group By
Signature
Annotation
Color By
Signature
Annotation
Sorting
Sort By
Total Counts
Sample Name
Signatures
Threshold
Aesthetic Settings
Same Y-axis Scale
X-axis Label
Legend
Plotly
Make Plot
Plot heatmap
Settings
Proportional
Show column names
Show row names
Z-score normalization
All Signatures
Selected Signatures
Samples
Annotate by
Annotation
Plot
Clustering Exposures
Explore Number of Clusters
Metric
Within Cluster Sum of Squares
Averaged Silhouette Coefficient
Gap Statisitc
Algorithm
k-means
Hierarchical
Hierarchical k-means
k-medoids
CLARA
Proportional
Explore
Clustering
Proportional
Clustering Algorithm
k-means
Hierarchical
Hierarchical k-means
k-medoids
CLARA
Clustering
Visualization
Group By
None
Signature
Annotation
Plotly
Visualize
Download musica result objects
Download Musica Object
Download Musica Result