campbio/musicatk
Mutational Signature Comprehensive Analysis Toolkit

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300
Source code
53
Man pages
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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
.gen_all_boots Source code
.get_average_error Source code
.get_indel_motifs Source code
.get_reconstruction_error Source code
.get_reconstruction_error_prop Source code
.get_reconstruction_error_raw Source code
.get_sil_width Source code
.gg_color_hue Source code
.gg_default_theme Source code
.iterative_discovery 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
.plot_result_model_signatures Source code
.required_maf_headers Source code
.required_musica_headers Source code
.resample_count_table Source code
.run_modified_kmeans 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
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_k_vals 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_from_counts Man page Source code
create_musica_from_variants Man page Source code
create_result_model Man page Source code
create_sbs192_table Man page Source code
create_sbs96_table Man page Source code
create_umap Man page Source code
credible_intervals Man page
credible_intervals,musica-method Man page
credible_intervals,result_collection-method Man page
credible_intervals,result_model-method Man page
credible_intervals<- Man page
credible_intervals<-,musica,matrix-method Man page
credible_intervals<-,result_collection,matrix-method Man page
credible_intervals<-,result_model,matrix-method Man page
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-method Man page
exposures,result_collection-method Man page
exposures,result_model-method Man page
exposures<- Man page
exposures<-,musica,matrix-method Man page
exposures<-,result_collection,matrix-method Man page
exposures<-,result_model,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 Man page Source code
get_count_type Source code
get_modality Man page
get_modality,musica-method Man page
get_modality,result_collection-method Man page
get_model Man page
get_model,musica-method Man page
get_model,result_collection-method Man page
get_result_list_entry Man page
get_result_list_entry,musica,character-method Man page
get_tab_name Source code
hyperparameter Man page
hyperparameter,musica-method Man page
hyperparameter,result_collection-method Man page
hyperparameter<- Man page
hyperparameter<-,musica,list-method Man page
hyperparameter<-,result_collection,list-method Man page
indel_musica Man page
k_select Man page Source code
lda_posterior Source code
metrics Man page
metrics,musica-method Man page
metrics,result_collection-method Man page
metrics,result_model-method Man page
metrics<- Man page
metrics<-,musica,SimpleList-method Man page
metrics<-,result_collection,SimpleList-method Man page
metrics<-,result_model,SimpleList-method Man page
modality Man page
modality,musica-method Man page
modality,result_collection-method Man page
modality,result_model-method Man page
modality<- Man page
modality<-,musica,matrix-method Man page
modality<-,result_collection,matrix-method Man page
modality<-,result_model,matrix-method Man page
model_id Man page
model_id,musica-method Man page
model_id,result_collection-method Man page
model_id,result_model-method Man page
model_id<- Man page
model_id<-,musica,matrix-method Man page
model_id<-,result_collection,matrix-method Man page
model_id<-,result_model,matrix-method Man page
musica Man page
musica-class Man page
musica_annot Man page
musica_sbs96 Man page
musica_sbs96_tiny Man page
musicatk Man page Source code
name_signatures Man page Source code
num_signatures Man page
num_signatures,musica-method Man page
num_signatures,result_collection-method Man page
num_signatures,result_model-method Man page
num_signatures<- Man page
num_signatures<-,musica,matrix-method Man page
num_signatures<-,result_collection,matrix-method Man page
num_signatures<-,result_model,matrix-method Man page
other_parameters Man page
other_parameters,musica-method Man page
other_parameters,result_collection-method Man page
other_parameters,result_model-method Man page
other_parameters<- Man page
other_parameters<-,musica,matrix-method Man page
other_parameters<-,result_collection,matrix-method Man page
other_parameters<-,result_model,matrix-method Man page
parameter Man page
parameter,musica-method Man page
parameter,result_collection-method Man page
parameter<- Man page
parameter<-,musica,list-method Man page
parameter<-,result_collection,list-method Man page
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_k_comparison 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
result_collection-class Man page
result_list Man page
result_list,musica-method Man page
result_list<- Man page
result_list<-,musica,SimpleList-method Man page
result_model-class Man page
samp_annot Man page
samp_annot,musica-method Man page
samp_annot<- Man page
samp_annot<-,musica,character,vector-method Man page
sample_names Man page
sample_names,musica-method Man page
select_genome Man page Source code
sig_compare Source code
signatures Man page
signatures,musica-method Man page
signatures,result_collection-method Man page
signatures,result_model-method Man page
signatures<- Man page
signatures<-,musica,matrix-method Man page
signatures<-,result_collection,matrix-method Man page
signatures<-,result_model,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,result_model-method Man page
tables Man page
tables,musica-method Man page
tables<- Man page
tables<-,musica,list-method Man page
umap Man page
umap,musica-method Man page
umap,result_collection-method Man page
umap,result_model-method Man page
umap<- Man page
umap<-,musica,matrix-method Man page
umap<-,result_collection,matrix-method Man page
umap<-,result_model,matrix-method Man page
variants Man page
variants,musica-method Man page
variants<- Man page
variants<-,musica,data.table-method Man page
campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.

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