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sigminer  

Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
View on CRAN: Click here


Download and install sigminer package within the R console
Install from CRAN:
install.packages("sigminer")

Install from Github:
library("remotes")
install_github("cran/sigminer")

Install by package version:
library("remotes")
install_version("sigminer", "2.3.0")



Attach the package and use:
library("sigminer")
Maintained by
Shixiang Wang
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-04-25
Latest Update: 2023-12-12
Description:
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.
How to cite:
Shixiang Wang (2019). sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations. R package version 2.3.0, https://cran.r-project.org/web/packages/sigminer
Previous versions and publish date:
0.1.9 (2019-04-25 13:00), 0.1.11 (2019-05-07 09:50), 1.0.0 (2020-03-31 17:00), 1.0.3 (2020-05-01 00:30), 1.0.5 (2020-05-14 19:10), 1.0.6 (2020-06-01 08:40), 1.0.7 (2020-06-17 07:20), 1.0.13 (2020-08-27 13:30), 1.0.16 (2020-09-12 16:30), 1.0.19 (2020-09-28 09:30), 1.1.0 (2020-11-11 08:40), 1.2.1 (2021-01-08 10:10), 1.2.4 (2021-01-31 01:30), 1.2.5 (2021-02-20 02:10), 2.0.0 (2021-04-01 14:50), 2.0.1 (2021-05-19 11:40), 2.0.2 (2021-06-17 13:10), 2.0.3 (2021-07-19 01:10), 2.0.4 (2021-08-03 14:10), 2.0.5 (2021-09-03 09:10), 2.1.0 (2021-09-22 12:00), 2.1.1 (2021-10-29 07:40), 2.1.2 (2021-12-15 08:50), 2.1.3 (2022-03-10 12:00), 2.1.4 (2022-04-26 10:40), 2.1.5 (2022-06-30 15:50), 2.1.6 (2022-08-09 17:20), 2.1.7 (2022-08-31 10:40), 2.1.8 (2022-10-20 08:40), 2.1.9 (2022-11-09 10:40), 2.2.0 (2023-04-06 11:00), 2.2.2 (2023-08-21 06:30), 2.3.0 (2023-12-12 12:50)
Other packages that cited sigminer R package
View sigminer citation profile
Other R packages that sigminer depends, imports, suggests or enhances
Functions, R codes and Examples using the sigminer R package
Some associated functions: CN.features . CopyNumber-class . MAF-class . add_h_arrow . add_labels . bp . centromeres.T2T . centromeres.hg19 . centromeres.hg38 . centromeres.mm10 . centromeres.mm9 . chromsize.T2T . chromsize.hg19 . chromsize.hg38 . chromsize.mm10 . chromsize.mm9 . cosine . cytobands.T2T . cytobands.hg19 . cytobands.hg38 . cytobands.mm10 . cytobands.mm9 . enrich_component_strand_bias . get_Aneuploidy_score . get_adj_p . get_bayesian_result . get_cn_freq_table . get_cn_ploidy . get_genome_annotation . get_group_comparison . get_groups . get_intersect_size . get_pLOH_score . get_shannon_diversity_index . get_sig_cancer_type_index . get_sig_db . get_sig_exposure . get_sig_feature_association . get_sig_rec_similarity . get_sig_similarity . get_tidy_association . group_enrichment . group_enrichment2 . handle_hyper_mutation . hello . output_bootstrap . output_fit . output_sig . output_tally . pipe . read_copynumber . read_copynumber_ascat . read_copynumber_seqz . read_maf . read_sv_as_rs . read_vcf . read_xena_variants . report_bootstrap_p_value . same_size_clustering . scoring . show_catalogue . show_cn_circos . show_cn_components . show_cn_distribution . show_cn_features . show_cn_freq_circos . show_cn_group_profile . show_cn_profile . show_cor . show_cosmic . show_cosmic_sig_profile . show_group_comparison . show_group_distribution . show_group_enrichment . show_group_mapping . show_groups . show_sig_bootstrap . show_sig_consensusmap . show_sig_exposure . show_sig_feature_corrplot . show_sig_fit . show_sig_profile . show_sig_profile_heatmap . show_sig_profile_loop . sig_auto_extract . sig_convert . sig_estimate . sig_extract . sig_fit . sig_fit_bootstrap . sig_fit_bootstrap_batch . sig_operation . sig_tally . sig_unify_extract . sigminer-package . sigprofiler . simulated_catalogs . simulation . subset.CopyNumber . tidyeval . transcript.T2T . transcript.hg19 . transcript.hg38 . transcript.mm10 . transcript.mm9 . transform_seg_table . use_color_style . 
Some associated R codes: CN-mutex-classification-method.R . RcppExports.R . add_h_arrow.R . add_labels.R . assert.R . bayesianNMF.R . best_practice.R . best_practice_helper.R . class.R . cosine.R . data.R . enrich_component_strand_bias.R . find_enriched_signature.R . generate_matrices.R . get.R . get_Aneuploidy_score.R . get_adj_p.R . get_bayesian_result.R . get_cn_freq_table.R . get_cn_ploidy.R . get_genome_annotation.R . get_group_comparison.R . get_groups.R . get_intersect_size.R . get_pLOH_score.R . get_reconstructed_similarity.R . get_shannon_diversity_index.R . get_sig_cancer_type_index.R . get_sig_db.R . get_sig_exposure.R . get_sig_feature_association.R . get_sig_optimal_exposure.R . get_sig_similarity.R . get_sv.R . get_tidy_association.R . globalVariables.R . group_enrichment.R . handle_hyper_mutation.R . hello.R . helper_create_chunks.R . helper_create_colormap.R . helper_derive_cn_features.R . helper_join_segments.R . helper_normalize_by_feature.R . helper_scale_nmf_matrix.R . helper_sort_signature.R . output.R . read_copynumber.R . read_copynumber_ascat.R . read_copynumber_seqz.R . read_maf.R . read_vcf.R . same_size_clustering.R . scoring.R . show_catalogue.R . show_cn_circos.R . show_cn_components.R . show_cn_distribution.R . show_cn_features.R . show_cn_freq_circos.R . show_cn_group_profile.R . show_cn_profile.R . show_cor.R . show_cosmic_signature.R . show_cosmic_signature_profile.R . show_group_comparison.R . show_group_distribution.R . show_group_enrichment.R . show_group_mapping.R . show_groups.R . show_sig_bootstrap.R . show_sig_consensusmap.R . show_sig_exposure.R . show_sig_feature_corrplot.R . show_sig_fit.R . show_sig_profile.R . show_sig_profile_heatmap.R . show_sig_profile_loop.R . sig_auto_extract.R . sig_convert.R . sig_estimate.R . sig_extract.R . sig_fit.R . sig_fit_bootstrap.R . sig_fit_bootstrap_batch.R . sig_tally.R . sig_unify_extract.R . sigflow.R . sigminer.R . signature_obj_operation.R . sigprofiler.R . simulation.R . transform_seg_table.R . utils-pipe.R . utils-tidy-eval.R . utils.R . utils_mem.R . zzz.R .  Full sigminer package functions and examples
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