Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Get Specified Bayesian NMF Result from Run
Get CNV Frequency Table
Get Ploidy from Absolute Copy Number Profile
Get Genome Annotation
Get Signature Exposure from 'Signature' Object
Class MAF
Get Curated Reference Signature Database
Output Signature Bootstrap Fitting Results
Add Horizontal Arrow with Text Label to a ggplot
Add Text Labels to a ggplot
Obtain Signature Index for Cancer Types
A Best Practice for Signature Extraction and Exposure (Activity) Attri...
Class CopyNumber
Calculate Cosine Measures
Performs Strand Bias Enrichment Analysis for a Given Sample-by-Compone...
Get Adjust P Values from Group Comparison
Get Aneuploidy Score from Copy Number Profile
Get Comparison Result between Signature Groups
Get Sample Groups from Signature Decomposition Information
Get Overlap Size between Interval x and y
Get proportions of pLOH score from Allele Specific Copy Number Profile
Get Shannon Diversity Index for Signatures
Calculate Association between Signature Exposures and Other Features
Get Reconstructed Profile Cosine Similarity, RSS, etc.
Calculate Similarity between Identified Signatures and Reference Signa...
Get Tidy Signature Association Results
General Group Enrichment Analysis
Group Enrichment Analysis with Subsets
Handle Hypermutant Samples
Say Hello to Users
Extract Signatures with SigProfiler
Output Signature Fitting Results
Output Signature Results
Output Tally Result in Barplots
Pipe operator
Read Absolute Copy Number Profile
Read Copy Number Data from ASCAT Result Files
Read Absolute Copy Number Profile from Sequenza Result Directory
Read MAF Files
Read Structural Variation Data as RS object
Read VCF Files as MAF Object
Read UCSC Xena Variant Format Data as MAF Object
Report P Values from bootstrap Results
Same Size Clustering
Score Copy Number Profile
Show Alteration Catalogue Profile
Show Copy Number Profile in Circos
Show Copy Number Components
Show Copy Number Distribution either by Length or Chromosome
Show Copy Number Feature Distributions
Show Copy Number Variation Frequency Profile with Circos
Show Summary Copy Number Profile for Sample Groups
Show Sample Copy Number Profile
A Simple and General Way for Association Analysis
Show Signature Information in Web Browser
Plot Reference (Mainly COSMIC) Signature Profile
Plot Group Comparison Result
Show Groupped Variable Distribution
Show Group Enrichment Result
Map Groups using Sankey
Show Signature Contribution in Clusters
Show Signature Bootstrap Analysis Results
Show Signature Consensus Map
Plot Signature Exposure
Draw Corrplot for Signature Exposures and Other Features
Show Signature Fit Result
Show Signature Profile
Show Signature Profile with Heatmap
Show Signature Profile with Loop Way
Extract Signatures through the Automatic Relevance Determination Techn...
Convert Signatures between different Genomic Distribution of Component...
Estimate Signature Number
Extract Signatures through NMF
Fit Signature Exposures with Linear Combination Decomposition
Obtain Bootstrap Distribution of Signature Exposures of a Certain Tumo...
Exposure Instability Analysis of Signature Exposures with Bootstrappin...
Obtain or Modify Signature Information
Tally a Genomic Alteration Object
An Unified Interface to Extract Signatures
sigminer: Extract, Analyze and Visualize Signatures for Genomic Variat...
Simulation Analysis
Subsetting CopyNumber object
Tidy eval helpers
Transform Copy Number Table
Set Color Style for Plotting
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Useful links