Man pages for sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

add_h_arrowAdd Horizontal Arrow with Text Label to a ggplot
add_labelsAdd Text Labels to a ggplot
bpA Best Practice for Signature Extraction and Exposure...
centromeres.hg19Location of Centromeres at Genome Build hg19
centromeres.hg38Location of Centromeres at Genome Build hg38
centromeres.mm10Location of Centromeres at Genome Build mm10
chromsize.hg19Chromosome Size of Genome Build hg19
chromsize.hg38Chromosome Size of Genome Build hg38
chromsize.mm10Chromosome Size of Genome Build mm10
CN.featuresClassification Table of Copy Number Features Devised by Wang...
CopyNumber-classClass CopyNumber
cosineCalculate Cosine Measures
cytobands.hg19Location of Chromosome Cytobands at Genome Build hg19
cytobands.hg38Location of Chromosome Cytobands at Genome Build hg38
cytobands.mm10Location of Chromosome Cytobands at Genome Build mm10
enrich_component_strand_biasPerforms Strand Bias Enrichment Analysis for a Given...
get_adj_pGet Adjust P Values from Group Comparison
get_bayesian_resultGet Specified Bayesian NMF Result from Run
get_cn_freq_tableGet CNV Frequency Table
get_cn_ploidyGet Ploidy from Absolute Copy Number Profile
get_genome_annotationGet Genome Annotation
get_group_comparisonGet Comparison Result between Signature Groups
get_groupsGet Sample Groups from Signature Decomposition Information
get_shannon_diversity_indexGet Shannon Diversity Index for Signatures
get_sig_cancer_type_indexObtain Signature Index for Cancer Types
get_sig_dbGet Curated Reference Signature Database
get_sig_exposureGet Signature Exposure from 'Signature' Object
get_sig_feature_associationCalculate Association between Signature Exposures and Other...
get_sig_rec_similarityGet Reconstructed Profile Cosine Similarity, RSS, etc.
get_sig_similarityCalculate Similarity between Identified Signatures and...
get_tidy_associationGet Tidy Signature Association Results
group_enrichmentGeneral Group Enrichment Analysis
handle_hyper_mutationHandle Hypermutant Samples
helloSay Hello to Users
MAF-classClass MAF
output_bootstrapOutput Signature Bootstrap Fitting Results
output_fitOutput Signature Fitting Results
output_sigOutput Signature Results
output_tallyOutput Tally Result in Barplots
pipePipe operator
read_copynumberRead Absolute Copy Number Profile
read_copynumber_seqzRead Absolute Copy Number Profile from Sequenza Result...
read_mafRead MAF Files
read_sv_as_rsRead Structural Variation Data as RS object
read_vcfRead VCF Files as MAF Object
read_xena_variantsRead UCSC Xena Variant Format Data as MAF Object
report_bootstrap_p_valueReport P Values from bootstrap Results
same_size_clusteringSame Size Clustering
scoringScore Copy Number Profile
show_catalogueShow Alteration Catalogue Profile
show_cn_circosShow Copy Number Profile in Circos
show_cn_componentsShow Copy Number Components
show_cn_distributionShow Copy Number Distribution either by Length or Chromosome
show_cn_featuresShow Copy Number Feature Distributions
show_cn_freq_circosShow Copy Number Variation Frequency Profile with Circos
show_cn_group_profileShow Summary Copy Number Profile for Sample Groups
show_cn_profileShow Sample Copy Number Profile
show_corA Simple and General Way for Association Analysis
show_cosmicShow Signature Information in Web Browser
show_cosmic_sig_profilePlot Reference (Mainly COSMIC) Signature Profile
show_group_comparisonPlot Group Comparison Result
show_group_distributionShow Groupped Variable Distribution
show_group_enrichmentShow Group Enrichment Result
show_group_mappingMap Groups using Sankey
show_groupsShow Signature Contribution in Clusters
show_sig_bootstrapShow Signature Bootstrap Analysis Results
show_sig_consensusmapShow Signature Consensus Map
show_sig_exposurePlot Signature Exposure
show_sig_feature_corrplotDraw Corrplot for Signature Exposures and Other Features
show_sig_fitShow Signature Fit Result
show_sig_profileShow Signature Profile
show_sig_profile_heatmapShow Signature Profile with Heatmap
show_sig_profile_loopShow Signature Profile with Loop Way
sig_auto_extractExtract Signatures through the Automatic Relevance...
sig_convertConvert Signatures between different Genomic Distribution of...
sig_estimateEstimate Signature Number
sig_extractExtract Signatures through NMF
sig_fitFit Signature Exposures with Linear Combination Decomposition
sig_fit_bootstrapObtain Bootstrap Distribution of Signature Exposures of a...
sig_fit_bootstrap_batchExposure Instability Analysis of Signature Exposures with...
sigminersigminer: Extract, Analyze and Visualize Signatures for...
sig_operationObtain or Modify Signature Information
sigprofilerExtract Signatures with SigProfiler
sig_tallyTally a Genomic Alteration Object
simulated_catalogsA List of Simulated SBS-96 Catalog Matrix
simulationSimulation Analysis
subset.CopyNumberSubsetting CopyNumber object
tidyevalTidy eval helpers
transcript.hg19Merged Transcript Location at Genome Build hg19
transcript.hg38Merged Transcript Location at Genome Build hg38
transcript.mm10Merged Transcript Location at Genome Build mm10
transform_seg_tableTransform Copy Number Table
use_color_styleSet Color Style for Plotting
sigminer documentation built on April 1, 2021, 5:06 p.m.