campbio/musicatk
Mutational Signature Comprehensive Analysis Toolkit

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Functions
213
Source code
47
Man pages
82
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campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit
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API

API for campbio/musicatk
Mutational Signature Comprehensive Analysis Toolkit

Global functions
%>% Man page
.addSmallLegend Source code
.add_annotation_to_df Source code
.check_headers Source code
.check_variant_genome Source code
.check_variant_ref_in_genome Source code
.cosine Source code
.cosineDist Source code
.count1 Source code
.count2_del Source code
.count2_ins Source code
.count_repeat Source code
.create_count_table Source code
.discrete_colors Source code
.extract_count_table Source code
.get_indel_motifs Source code
.gg_color_hue Source code
.gg_default_theme Source code
.jsd Man page Source code
.kld Source code
.micro_left Source code
.micro_right Source code
.multi_modal_discovery Source code
.overwrite_samp_annot Source code
.pivot_exposures Source code
.pivot_signatures Source code
.plot_compare_result_signatures Source code
.required_maf_headers Source code
.required_musica_headers Source code
.subset_count_tables Source code
.table_exists_warning Source code
add_flank_to_variants Man page Source code
add_variant_type Man page Source code
annotate_replication_strand Man page Source code
annotate_transcript_strand Man page Source code
annotate_variant_length Man page Source code
annotate_variant_type Man page Source code
auto_predict_grid Man page Source code
auto_subset_sigs Man page Source code
build_custom_table Man page Source code
build_standard_table Man page Source code
built_tables Man page
built_tables,musica-method Man page
built_tables,musica_result-method Man page
cluster_exposure Man page Source code
combine_count_tables Man page Source code
combine_predict_grid Man page Source code
compare_cosmic_v2 Man page Source code
compare_cosmic_v3 Man page Source code
compare_results Man page Source code
cosmic_v2_sigs Man page
cosmic_v2_subtype_map Man page Source code
cosmic_v3_dbs_sigs Man page
cosmic_v3_indel_sigs Man page
cosmic_v3_sbs_sigs Man page
cosmic_v3_sbs_sigs_exome Man page
count_table-class Man page
create_dbs78_table Man page Source code
create_ind83_table Source code
create_musica Man page Source code
create_sbs192_table Man page Source code
create_sbs96_table Man page Source code
create_umap Man page Source code
dbs_musica Man page
discover_signatures Man page Source code
drop_annotation Man page Source code
drop_count_table Source code
drop_na_variants Source code
exposure_differential_analysis Man page Source code
exposures Man page
exposures,musica_result-method Man page
exposures<- Man page
exposures<-,musica_result,matrix-method Man page
extract_count_tables Man page Source code
extract_variants Man page Source code
extract_variants_from_maf Man page Source code
extract_variants_from_maf_file Man page Source code
extract_variants_from_matrix Man page Source code
extract_variants_from_vcf Man page Source code
extract_variants_from_vcf_file Man page Source code
generate_result_grid Man page Source code
get_annot_tab Source code
get_color_mapping Source code
get_count_features Source code
get_count_table Source code
get_count_type Source code
get_grid_list Source code
get_grid_params Source code
get_grid_table Source code
get_musica Man page
get_musica,musica_result-method Man page
get_result_alg Source code
get_tab_name Source code
indel_musica Man page
k_select Man page Source code
lda_posterior Source code
musica Man page
musica-class Man page
musica_annot Man page
musica_result-class Man page
musica_result_grid-class Man page
musica_sbs96 Man page
musica_sbs96_tiny Man page
musicatk Man page Source code
name_signatures Man page Source code
plot_cluster Man page Source code
plot_differential_analysis Man page Source code
plot_exposures Man page Source code
plot_heatmap Man page Source code
plot_sample_counts Man page Source code
plot_sample_reconstruction_error Man page Source code
plot_signatures Man page Source code
plot_umap Man page Source code
predict_decompTumor2Sig Source code
predict_exposure Man page Source code
rc Man page Source code
reconstruct_sample Source code
rep_range Man page
res Man page
res_annot Man page
samp_annot Man page
samp_annot,musica-method Man page
samp_annot,musica_result-method Man page
samp_annot<- Man page
samp_annot<-,musica,character,vector-method Man page
samp_annot<-,musica_result,character,vector-method Man page
sample_names Man page
sample_names,musica-method Man page
sample_names,musica_result-method Man page
select_genome Man page Source code
set_grid_list Source code
set_grid_params Source code
set_grid_table Source code
sig_compare Source code
signatures Man page
signatures,musica_result-method Man page
signatures<- Man page
signatures<-,musica_result,matrix-method Man page
subset_musica_by_annotation Man page Source code
subset_musica_by_counts Man page Source code
subset_variant_by_type Man page Source code
subset_variants_by_samples Man page Source code
table_96 Man page Source code
table_selected Man page
table_selected,musica_result-method Man page
tables Man page
tables,musica-method Man page
tables,musica_result-method Man page
tables<- Man page
tables<-,musica,list-method Man page
umap Man page
umap,musica_result-method Man page
umap<- Man page
umap<-,musica_result,matrix-method Man page
variants Man page
variants,musica-method Man page
variants,musica_result-method Man page
variants<- Man page
variants<-,musica,data.table-method Man page
whichSignatures Source code
campbio/musicatk documentation built on Oct. 22, 2023, 8:28 p.m.

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