API for sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Global functions
%>% Man page
.collapse_segTab Source code
.data Man page
.env Man page
.onAttach Source code
.onLoad Source code
:= Man page
BayesNMF.L1.KL.fixed_W.Z Source code
BayesNMF.L1.KL.fixed_W.Z.sample Source code
BayesNMF.L1KL Source code
BayesNMF.L1W.L2H Source code
BayesNMF.L2KL Source code
CN.features Man page
CopyNumber Man page
CopyNumber-class Man page
FrobeniusNorm Source code
MAF Man page
MAF-class Man page
`%:::%` Source code
add_h_arrow Man page Source code
add_labels Man page Source code
as_label Man page
as_name Man page
assert_class Source code
bootstrap_p_value Source code
bp Man page
bp_attribute_activity Man page
bp_cluster_iter_list Man page
bp_extract_signatures Man page Source code
bp_extract_signatures_iter Man page
bp_get_clustered_sigs Man page
bp_get_rank_score Man page
bp_get_sig_obj Man page
bp_get_stats Man page
bp_show_survey Man page
bp_show_survey2 Man page
build_chrom_coordinate Source code
build_opps_matrix Source code
call_component Source code
call_component_sv Source code
centromeres.hg19 Man page
centromeres.hg38 Man page
centromeres.mm10 Man page
check_nmf_matrix Source code
chromsize.hg19 Man page
chromsize.hg38 Man page
chromsize.mm10 Man page
chunk2 Source code
col2hex Source code
collapse_hyper_records Source code
cosine Man page Source code
cosineMatrix Source code
cosineVector Source code
count_components Source code
count_components_wrapper Source code
cytobands.hg19 Man page
cytobands.hg38 Man page
cytobands.mm10 Man page
decompose_NNLS Source code
decompose_QP Source code
decompose_SA Source code
deploy_sigflow Source code
enquo Man page
enquos Man page
enrich_component_strand_bias Man page Source code
enrich_one Source code
expr Man page
file_name Source code
find_enriched_signature Source code
generate_matrix_SBS Source code
getAB Source code
getBP10MB_v2 Source code
getBPnum Source code
getBoChr Source code
getCN Source code
getCN_v2 Source code
getCS Source code
getCentromereDistCounts Source code
getChangepointCN Source code
getClustered Source code
getDists Source code
getLOH Source code
getNC50 Source code
getNChrV Source code
getOscilation Source code
getRearrSize Source code
getSegsize Source code
getSegsize_v2 Source code
getType Source code
get_3d_array_stats Source code
get_ArmLocation Source code
get_LengthFraction Source code
get_adj_p Man page Source code
get_bayesian_result Man page Source code
get_cn_freq_table Man page Source code
get_cn_ploidy Man page Source code
get_cnlist Source code
get_cnsummary_sample Source code
get_components_mutex Source code
get_components_sv Source code
get_expo_corr_stat Source code
get_feature_components Source code
get_features_mutex Source code
get_features_sv Source code
get_features_wang Source code
get_genome_annotation Man page Source code
get_group_comparison Man page Source code
get_groups Man page Source code
get_matrix_mutex Source code
get_matrix_sv Source code
get_segsize_order Source code
get_shannon_diversity_index Man page Source code
get_sig_cancer_type_index Man page Source code
get_sig_db Man page Source code
get_sig_exposure Man page Source code
get_sig_feature_association Man page Source code
get_sig_rec_similarity Man page Source code
get_sig_similarity Man page Source code
get_similarity_stats Source code
get_stat_samps Source code
get_stat_sigs Source code
get_svclass Source code
get_svlist Source code
get_tidy_association Man page Source code
get_timestamp Source code
group_enrichment Man page Source code
handle_hyper_mutation Man page Source code
handle_sex Source code
hcbottom Source code
hello Man page Source code
helper_create_chunks Source code
helper_create_colormap Source code
helper_join_segments2 Source code
helper_normalize_by_feature Source code
helper_scale_nmf_matrix Source code
helper_sort_signature Source code
human_trinuc_freqs Source code
is.wholenumber Source code
isValidAndUnreserved Source code
kmvar Source code
mem_used Source code
mutate_cond Source code
my.t.test.p.value Source code
nnit Source code
node_size Source code
norm2rg Source code
normalize_solution Source code
output_bootstrap Man page Source code
output_fit Man page Source code
output_sig Man page Source code
output_tally Man page Source code
pairwise.fisher.test Source code
parse_cosmic Source code
plot_cn_circos Source code
plot_cn_circos_density Source code
plot_cn_profile Source code
plot_cn_summary Source code
plot_enrichment_simple Source code
print.bytes Source code
process_solution Source code
query_remote_data Source code
quote_opt Source code
read_copynumber Man page Source code
read_copynumber_seqz Man page Source code
read_maf Man page Source code
read_sigprofiler_solution Source code
read_sv_as_rs Man page Source code
read_vcf Man page Source code
read_xena_variants Man page Source code
report_bootstrap_p_value Man page Source code
return_expo Source code
rgb2hex Source code
same_size_clustering Man page Source code
scoring Man page Source code
scoring_Chromoth Source code
scoring_MACN Source code
scoring_TD Source code
send_elapsed_time Source code
send_error Source code
send_info Source code
send_stop Source code
send_success Source code
send_warning Source code
set_future_strategy Source code
shifter Source code
show_bytes Source code
show_catalogue Man page Source code
show_cn_circos Man page Source code
show_cn_components Man page Source code
show_cn_distribution Man page Source code
show_cn_features Man page Source code
show_cn_freq_circos Man page Source code
show_cn_group_profile Man page Source code
show_cn_profile Man page Source code
show_cor Man page Source code
show_cosmic Man page Source code
show_cosmic_sig_profile Man page Source code
show_group_comparison Man page Source code
show_group_distribution Man page Source code
show_group_enrichment Man page Source code
show_group_mapping Man page Source code
show_groups Man page Source code
show_sig_bootstrap Man page
show_sig_bootstrap_error Man page Source code
show_sig_bootstrap_exposure Man page Source code
show_sig_bootstrap_stability Man page Source code
show_sig_consensusmap Man page Source code
show_sig_exposure Man page Source code
show_sig_feature_corrplot Man page Source code
show_sig_fit Man page Source code
show_sig_number_survey Man page Source code
show_sig_number_survey2 Man page Source code
show_sig_profile Man page Source code
show_sig_profile_heatmap Man page Source code
show_sig_profile_loop Man page Source code
sig_attrs Man page Source code
sig_auto_extract Man page Source code
sig_convert Man page Source code
sig_estimate Man page Source code
sig_exposure Man page Source code
sig_extract Man page Source code
sig_fit Man page Source code
sig_fit_bootstrap Man page Source code
sig_fit_bootstrap_batch Man page Source code
sig_modify_names Man page Source code
sig_names Man page Source code
sig_number Man page Source code
sig_operation Man page
sig_signature Man page Source code
sig_tally Man page Source code
sig_tally.CopyNumber Man page Source code
sig_tally.MAF Man page Source code
sig_tally.RS Man page Source code
sigminer Man page
sigprofiler Man page
sigprofiler_extract Man page Source code
sigprofiler_import Man page Source code
simulate_catalogue Man page Source code
simulate_catalogue_matrix Man page Source code
simulate_signature Man page Source code
simulated_catalogs Man page
simulation Man page
split_seq Source code
subset.CopyNumber Man page Source code
sym Man page
syms Man page
tf_signature Source code
tidyeval Man page
transcript.hg19 Man page
transcript.hg38 Man page
transcript.mm10 Man page
transform_seg_table Man page Source code
use_color_style Man page Source code
validate_segTab Source code
sigminer documentation built on April 1, 2021, 5:06 p.m.