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Sigminer: Mutational Signature Analysis and Visualization in R

:bar_chart: Overview

The cancer genome is shaped by various mutational processes over its lifetime, stemming from exogenous and cell-intrinsic DNA damage, and error-prone DNA replication, leaving behind characteristic mutational spectra, termed mutational signatures. This package, sigminer, helps users to extract, analyze and visualize signatures from genome alteration records, thus providing new insight into cancer study.

For pipeline tool, please see its co-evolutionary CLI sigflow.

SBS signatures:

Copy number signatures:

DBS signatures:

INDEL (i.e. ID) signatures:

Genome rearrangement signatures:

:airplane: Features

  • supports a standard de novo pipeline for identification of 5 types of signatures: copy number, SBS, DBS, INDEL and RS (genome rearrangement signature).
  • supports quantify exposure for one sample based on known signatures.
  • supports association and group analysis and visualization for signatures.
  • supports two types of signature exposures: relative exposure (relative contribution of signatures in each sample) and absolute exposure (estimated variation records of signatures in each sample).
  • supports basic summary and visualization for profile of mutation (powered by maftools) and copy number.
  • supports parallel computation by R packages foreach, future and NMF.
  • efficient code powered by R packages data.table and tidyverse.
  • elegant plots powered by R packages ggplot2, ggpubr, cowplot and patchwork.
  • well tested by R package testthat and documented by R package roxygen2, roxytest, pkgdown, and etc. for both reliable and reproducible research.

:arrow_double_down: Installation

You can install the stable release of sigminer from CRAN with:

install.packages("BiocManager")
BiocManager::install("sigminer", dependencies = TRUE)

You can install the development version of sigminer from Github with:

remotes::install_github("ShixiangWang/sigminer", dependencies = TRUE)
# For Chinese users, run 
remotes::install_git("https://gitee.com/ShixiangWang/sigminer", dependencies = TRUE)

You can also install sigminer from conda bioconda channel with

# Please note version number of the bioconda release

# You can install an individual environment firstly with
# conda create -n sigminer
# conda activate sigminer
conda install -c bioconda -c conda-forge r-sigminer

:beginner: Usage

A complete documentation of sigminer can be read online at https://shixiangwang.github.io/sigminer-book/. All functions are well organized and documented at https://shixiangwang.github.io/sigminer/reference/index.html. For usage of a specific function fun, run ?fun in your R console to see its documentation.

:paperclip: Citation

If you use sigminer in academic field, please cite one of the following papers.


  • Wang S, Li H, Song M, Tao Z, Wu T, He Z, et al. (2021) Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PLoS Genet 17(5): e1009557. https://doi.org/10.1371/journal.pgen.1009557

  • Shixiang Wang, Ziyu Tao, Tao Wu, Xue-Song Liu, Sigflow: An Automated And Comprehensive Pipeline For Cancer Genome Mutational Signature Analysis, Bioinformatics, btaa895. https://doi.org/10.1093/bioinformatics/btaa895


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:page_with_curl: References

Please properly cite the following references when you are using any corresponding features. The references are also listed in the function documentation. Very thanks to the works, sigminer cannot be created without the giants.

  1. Mayakonda, Anand, et al. “Maftools: efficient and comprehensive analysis of somatic variants in cancer.” Genome research 28.11 (2018): 1747-1756.
  2. Gaujoux, Renaud, and Cathal Seoighe. “A Flexible R Package for Nonnegative Matrix Factorization.”" BMC Bioinformatics 11, no. 1 (December 2010).
  3. H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
  4. Kim, Jaegil, et al. “Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors.” Nature genetics 48.6 (2016): 600.
  5. Alexandrov, Ludmil B., et al. “Deciphering signatures of mutational processes operative in human cancer.” Cell reports 3.1 (2013): 246-259.
  6. Degasperi, Andrea, et al. “A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies.” Nature cancer 1.2 (2020): 249-263.
  7. Alexandrov, Ludmil B., et al. “The repertoire of mutational signatures in human cancer.” Nature 578.7793 (2020): 94-101.
  8. Macintyre, Geoff, et al. “Copy number signatures and mutational processes in ovarian carcinoma.” Nature genetics 50.9 (2018): 1262.
  9. Tan, Vincent YF, and Cédric Févotte. “Automatic relevance determination in nonnegative matrix factorization with the/spl beta/-divergence.” IEEE Transactions on Pattern Analysis and Machine Intelligence 35.7 (2012): 1592-1605.
  10. Bergstrom EN, Huang MN, Mahto U, Barnes M, Stratton MR, Rozen SG, Alexandrov LB: SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics 2019, 20:685 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6041-2

:page_facing_up: LICENSE

The software is made available for non commercial research purposes only under the MIT. However, notwithstanding any provision of the MIT License, the software currently may not be used for commercial purposes without explicit written permission after contacting Shixiang Wang wangshx@shanghaitech.edu.cn or Xue-Song Liu liuxs@shanghaitech.edu.cn.

MIT © 2019-Present Shixiang Wang, Xue-Song Liu

MIT © 2018 Anand Mayakonda


Cancer Biology Group @ShanghaiTech

Research group led by Xue-Song Liu in ShanghaiTech University

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Install

install.packages('sigminer')

Monthly Downloads

466

Version

2.1.0

License

MIT + file LICENSE

Issues

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Stars

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Maintainer

Shixiang Wang

Last Published

September 22nd, 2021

Functions in sigminer (2.1.0)

cytobands.hg38

Location of Chromosome Cytobands at Genome Build hg38
chromsize.hg38

Chromosome Size of Genome Build hg38
get_pLOH_score

Get proportions of pLOH score from Allele Specific Copy Number Profile
get_intersect_size

Get Overlap Size between Interval x and y
chromsize.hg19

Chromosome Size of Genome Build hg19
cosine

Calculate Cosine Measures
get_group_comparison

Get Comparison Result between Signature Groups
get_shannon_diversity_index

Get Shannon Diversity Index for Signatures
cytobands.hg19

Location of Chromosome Cytobands at Genome Build hg19
get_groups

Get Sample Groups from Signature Decomposition Information
bp

A Best Practice for Signature Extraction and Exposure (Activity) Attribution
cytobands.mm10

Location of Chromosome Cytobands at Genome Build mm10
get_sig_cancer_type_index

Obtain Signature Index for Cancer Types
output_fit

Output Signature Fitting Results
get_bayesian_result

Get Specified Bayesian NMF Result from Run
enrich_component_strand_bias

Performs Strand Bias Enrichment Analysis for a Given Sample-by-Component Matrix
get_genome_annotation

Get Genome Annotation
cytobands.mm9

Location of Chromosome Cytobands at Genome Build mm9
get_cn_ploidy

Get Ploidy from Absolute Copy Number Profile
get_cn_freq_table

Get CNV Frequency Table
handle_hyper_mutation

Handle Hypermutant Samples
read_maf

Read MAF Files
group_enrichment

General Group Enrichment Analysis
read_sv_as_rs

Read Structural Variation Data as RS object
read_copynumber_seqz

Read Absolute Copy Number Profile from Sequenza Result Directory
output_sig

Output Signature Results
get_adj_p

Get Adjust P Values from Group Comparison
get_Aneuploidy_score

Get Aneuploidy Score from Copy Number Profile
get_sig_db

Get Curated Reference Signature Database
output_tally

Output Tally Result in Barplots
show_cn_components

Show Copy Number Components
get_sig_exposure

Get Signature Exposure from 'Signature' Object
%>%

Pipe operator
show_cn_distribution

Show Copy Number Distribution either by Length or Chromosome
get_sig_feature_association

Calculate Association between Signature Exposures and Other Features
get_sig_rec_similarity

Get Reconstructed Profile Cosine Similarity, RSS, etc.
same_size_clustering

Same Size Clustering
read_vcf

Read VCF Files as MAF Object
hello

Say Hello to Users
show_group_enrichment

Show Group Enrichment Result
show_group_distribution

Show Groupped Variable Distribution
show_groups

Show Signature Contribution in Clusters
show_cn_profile

Show Sample Copy Number Profile
read_xena_variants

Read UCSC Xena Variant Format Data as MAF Object
output_bootstrap

Output Signature Bootstrap Fitting Results
show_group_mapping

Map Groups using Sankey
scoring

Score Copy Number Profile
show_cn_group_profile

Show Summary Copy Number Profile for Sample Groups
report_bootstrap_p_value

Report P Values from bootstrap Results
sig_tally

Tally a Genomic Alteration Object
show_sig_exposure

Plot Signature Exposure
show_sig_profile_heatmap

Show Signature Profile with Heatmap
chromsize.mm9

Chromosome Size of Genome Build mm9
get_tidy_association

Get Tidy Signature Association Results
read_copynumber_ascat

Read Copy Number Data from ASCAT Result Files
chromsize.mm10

Chromosome Size of Genome Build mm10
show_catalogue

Show Alteration Catalogue Profile
read_copynumber

Read Absolute Copy Number Profile
get_sig_similarity

Calculate Similarity between Identified Signatures and Reference Signatures
show_cosmic_sig_profile

Plot Reference (Mainly COSMIC) Signature Profile
show_group_comparison

Plot Group Comparison Result
show_sig_profile_loop

Show Signature Profile with Loop Way
show_cn_features

Show Copy Number Feature Distributions
simulated_catalogs

A List of Simulated SBS-96 Catalog Matrix
transform_seg_table

Transform Copy Number Table
use_color_style

Set Color Style for Plotting
sig_unify_extract

An Unified Interface to Extract Signatures
simulation

Simulation Analysis
tidyeval

Tidy eval helpers
show_sig_profile

Show Signature Profile
show_sig_fit

Show Signature Fit Result
subset.CopyNumber

Subsetting CopyNumber object
sig_fit_bootstrap_batch

Exposure Instability Analysis of Signature Exposures with Bootstrapping
show_sig_feature_corrplot

Draw Corrplot for Signature Exposures and Other Features
show_cn_circos

Show Copy Number Profile in Circos
show_cor

A Simple and General Way for Association Analysis
show_cn_freq_circos

Show Copy Number Variation Frequency Profile with Circos
show_sig_bootstrap

Show Signature Bootstrap Analysis Results
sig_fit

Fit Signature Exposures with Linear Combination Decomposition
show_cosmic

Show Signature Information in Web Browser
sig_operation

Obtain or Modify Signature Information
sigprofiler

Extract Signatures with SigProfiler
sigminer

sigminer: Extract, Analyze and Visualize Signatures for Genomic Variations
sig_convert

Convert Signatures between different Genomic Distribution of Components
transcript.hg19

Merged Transcript Location at Genome Build hg19
sig_auto_extract

Extract Signatures through the Automatic Relevance Determination Technique
sig_extract

Extract Signatures through NMF
show_sig_consensusmap

Show Signature Consensus Map
sig_estimate

Estimate Signature Number
transcript.mm9

Merged Transcript Location at Genome Build mm9
transcript.mm10

Merged Transcript Location at Genome Build mm10
sig_fit_bootstrap

Obtain Bootstrap Distribution of Signature Exposures of a Certain Tumor Sample
transcript.hg38

Merged Transcript Location at Genome Build hg38
add_h_arrow

Add Horizontal Arrow with Text Label to a ggplot
centromeres.hg38

Location of Centromeres at Genome Build hg38
centromeres.mm9

Location of Centromeres at Genome Build mm9
MAF-class

Class MAF
centromeres.hg19

Location of Centromeres at Genome Build hg19
add_labels

Add Text Labels to a ggplot
CN.features

Classification Table of Copy Number Features Devised by Wang et al. for Method 'W'
CopyNumber-class

Class CopyNumber
centromeres.mm10

Location of Centromeres at Genome Build mm10