url: https://shixiangwang.github.io/sigminer

home:
  title: Mutational Signature Miner in R

template:
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destination: docs

authors:
  Shixiang Wang:
    href: https://orcid.org/0000-0001-9855-7357
  Xue-Song Liu:
    href: https://orcid.org/0000-0002-7736-0077
reference:
  - title: Data input, classes and operation
    desc: Read genomic variation data as an R object and more.
    contents:
    - read_copynumber
    - read_copynumber_seqz
    - read_copynumber_ascat
    - read_maf
    - read_sv_as_rs
    - read_vcf
    - read_xena_variants
    - CopyNumber-class
    - MAF-class
    - subset.CopyNumber
  - title: Core pipeline 1 - de novo signature identification
    desc: Identify signatures from genomic variation profile. After reading data, the following functions construct the standard pipeline for most users.
    contents:
    - sig_tally
    - handle_hyper_mutation
    - sig_estimate
    #- show_sig_number_survey
    #- show_sig_number_survey2
    - sig_unify_extract
    - sig_extract
    - sig_auto_extract
    - sigprofiler
    - bp_attribute_activity
    #- bp_cluster_iter_list
    #- bp_extract_signatures
    #- bp_extract_signatures_iter
    #- bp_get_rank_score
    #- bp_get_sig_obj
    #- bp_get_stats
    #- bp_show_survey
    #- bp_show_survey2
  - title: Core pipeline 2 - signature exposure fitting and optimization
    desc: Quantify exposure in at least one sample with reference signatures. It can also be used to optimize signature exposure from pipeline 1 and analyze exposure instability.
    contents:
    - sig_tally
    - handle_hyper_mutation
    - get_sig_cancer_type_index
    - sig_fit
    - sig_fit_bootstrap
    - sig_fit_bootstrap_batch
    - report_bootstrap_p_value
  - title: Signature visualization
    desc: Show signature profile and exposure.
    contents:
    - show_catalogue
    - show_sig_profile
    - show_sig_profile_loop
    - show_sig_profile_heatmap
    - show_sig_exposure
    - show_cosmic
    - show_cosmic_sig_profile
    - show_sig_consensusmap
  - title: Fit and bootstrap visualization
    desc: Show signature fit and bootstrap analysis results.
    contents:
    - show_sig_fit
    - show_sig_bootstrap_exposure
    #- show_sig_bootstrap_error
    #- show_sig_bootstrap_stability
  - title: Output analysis results to local machine
    desc: Save results and plots as files. For automatic analysis, please use [sigflow](https://github.com/ShixiangWang/sigminer.workflow).
    contents:
    - output_tally
    - output_sig
    - output_fit
    - output_bootstrap
  - title: Signature object operation
    desc: Obtain or modify `Signature` object information.
    contents:
    - sig_names
    #- sig_modify_names
    #- sig_number
    #- sig_attrs
    #- sig_signature
    #- sig_exposure
  - title: Signature analysis and corresponding visualization
    desc: Analyze signatures and output the result to visualization.
    contents:
    - get_sig_similarity
    - get_sig_rec_similarity
    - get_sig_exposure
    - get_sig_feature_association
    - get_tidy_association
    - show_cor
    - show_sig_feature_corrplot
    - show_groups
    - get_groups
    - get_group_comparison
    - show_group_comparison
    - group_enrichment
    - show_group_enrichment
    - group_enrichment2
    - show_group_distribution
    - show_group_mapping
    - enrich_component_strand_bias
    - simulation
    - get_shannon_diversity_index
  - title: Package datasets
    desc: Datasets used for signature identification and analysis (some stored in `extdata/`).
    contents:
    - simulated_catalogs
    - CN.features
    - centromeres.hg19
    - centromeres.hg38
    - centromeres.mm10
    - centromeres.mm9
    - chromsize.hg19
    - chromsize.hg38
    - chromsize.mm10
    - - chromsize.mm9
    - cytobands.hg19
    - cytobands.hg38
    - cytobands.mm10
    - cytobands.mm9
    - transcript.hg19
    - transcript.hg38
    - transcript.mm10
    - transcript.mm9
  - title: Helpers
    desc: Helper functions used in the sigminer package.
    contents:
    - get_sig_db
    - sig_convert
    - get_genome_annotation
    - get_bayesian_result
    - get_adj_p
    - use_color_style
    - add_h_arrow
    - add_labels
    - cosine
    - get_cn_freq_table
    - same_size_clustering
    - get_intersect_size
  - title: Copy number analysis and visualization
    desc: Functions for analyzing copy number data and visualization.
    contents:
    - transform_seg_table
    - get_cn_ploidy
    - get_Aneuploidy_score
    - get_pLOH_score
    - scoring
    - show_cn_profile
    - show_cn_circos
    - show_cn_group_profile
    - show_cn_freq_circos
    - show_cn_distribution
    - show_cn_features
    - show_cn_components
  - title: Extra documentation
    desc: Extra function and introduction.
    contents:
    - hello
    - sigminer