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Shixiang Wang (王诗翔)

update readme

Jun 7, 2024

01d1e93 · Jun 7, 2024

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Name		Name	Last commit message	Last commit date
parent directory ..
figures		figures	update readme	Jun 7, 2024
CN.features.Rd		CN.features.Rd	✨ add new internal dataset simulated_catalogs & fix typo	Nov 19, 2020
CopyNumber-class.Rd		CopyNumber-class.Rd	Rewrite from read to derive	Sep 9, 2019
MAF-class.Rd		MAF-class.Rd	Rewrite from read to derive	Sep 9, 2019
add_h_arrow.Rd		add_h_arrow.Rd	Add add_labels & fix bug in get similarity	Jan 8, 2020
add_labels.Rd		add_labels.Rd	Fix doc error	Sep 21, 2020
bp.Rd		bp.Rd	update docs	Mar 27, 2023
centromeres.T2T.Rd		centromeres.T2T.Rd	update docs and change doc site deploy way	Dec 12, 2023
centromeres.hg19.Rd		centromeres.hg19.Rd	Rename as sig_fit	Mar 20, 2020
centromeres.hg38.Rd		centromeres.hg38.Rd	Rename as sig_fit	Mar 20, 2020
centromeres.mm10.Rd		centromeres.mm10.Rd	✨ clean mouse genome data and set how to get them	Jun 23, 2020
centromeres.mm9.Rd		centromeres.mm9.Rd	update docs	Mar 27, 2023
chromsize.T2T.Rd		chromsize.T2T.Rd	update docs and change doc site deploy way	Dec 12, 2023
chromsize.hg19.Rd		chromsize.hg19.Rd	Rename as sig_fit	Mar 20, 2020
chromsize.hg38.Rd		chromsize.hg38.Rd	Rename as sig_fit	Mar 20, 2020
chromsize.mm10.Rd		chromsize.mm10.Rd	✨ clean mouse genome data and set how to get them	Jun 23, 2020
chromsize.mm9.Rd		chromsize.mm9.Rd	update doc	May 18, 2021
cosine.Rd		cosine.Rd	update work	Nov 15, 2020
cytobands.T2T.Rd		cytobands.T2T.Rd	update docs and change doc site deploy way	Dec 12, 2023
cytobands.hg19.Rd		cytobands.hg19.Rd	Rename as sig_fit	Mar 20, 2020
cytobands.hg38.Rd		cytobands.hg38.Rd	Rename as sig_fit	Mar 20, 2020
cytobands.mm10.Rd		cytobands.mm10.Rd	✨ clean mouse genome data and set how to get them	Jun 23, 2020
cytobands.mm9.Rd		cytobands.mm9.Rd	update doc	May 18, 2021
enrich_component_strand_bias.Rd		enrich_component_strand_bias.Rd	Fix T U methdo and add enrich analysis for T/U	Apr 20, 2020
get_Aneuploidy_score.Rd		get_Aneuploidy_score.Rd	Add a new option to calc aneuploidy score, related to #374	Aug 13, 2021
get_adj_p.Rd		get_adj_p.Rd	Fix #74	Nov 25, 2019
get_bayesian_result.Rd		get_bayesian_result.Rd	Try roxytest #115	Mar 13, 2020
get_cn_freq_table.Rd		get_cn_freq_table.Rd	✨ clean code and add resolution factor	Aug 24, 2020
get_cn_ploidy.Rd		get_cn_ploidy.Rd	Try roxytest #115	Mar 13, 2020
get_genome_annotation.Rd		get_genome_annotation.Rd	set up t2t support	Dec 12, 2023
get_group_comparison.Rd		get_group_comparison.Rd	update	Sep 5, 2021
get_groups.Rd		get_groups.Rd	Try fixing action test	Nov 21, 2020
get_intersect_size.Rd		get_intersect_size.Rd	Add get_intersect_size	Aug 23, 2021
get_pLOH_score.Rd		get_pLOH_score.Rd	dont test get_pLOH_score()	Jul 7, 2023
get_shannon_diversity_index.Rd		get_shannon_diversity_index.Rd	Close #333	Jan 19, 2021
get_sig_cancer_type_index.Rd		get_sig_cancer_type_index.Rd	Add keyword option	Sep 9, 2020
get_sig_db.Rd		get_sig_db.Rd	Add the new signature and update reference	Mar 17, 2023
get_sig_exposure.Rd		get_sig_exposure.Rd	Close #285	Sep 29, 2020
get_sig_feature_association.Rd		get_sig_feature_association.Rd	删除 M 法	Feb 22, 2021
get_sig_rec_similarity.Rd		get_sig_rec_similarity.Rd	Added RSS and unexplained variance calculation in `get_sig_rec_simila…	Mar 11, 2021
get_sig_similarity.Rd		get_sig_similarity.Rd	update doc	Nov 14, 2023
get_tidy_association.Rd		get_tidy_association.Rd	Close #95 #96	Dec 30, 2019
group_enrichment.Rd		group_enrichment.Rd	Move plotting to donttest block	Jul 7, 2023
group_enrichment2.Rd		group_enrichment2.Rd	add group_enrichment2	Aug 17, 2022
handle_hyper_mutation.Rd		handle_hyper_mutation.Rd	Close #101	Jan 7, 2020
hello.Rd		hello.Rd	Add related docs	Sep 11, 2019
output_bootstrap.Rd		output_bootstrap.Rd	Add the new signature and update reference	Mar 17, 2023
output_fit.Rd		output_fit.Rd	Add the new signature and update reference	Mar 17, 2023
output_sig.Rd		output_sig.Rd	Add the new signature and update reference	Mar 17, 2023
output_tally.Rd		output_tally.Rd	Add output_* funs from sigflow	Sep 2, 2020
pipe.Rd		pipe.Rd	⚠️ Try fix cran checking warning	Jun 16, 2020
read_copynumber.Rd		read_copynumber.Rd	set up t2t support	Dec 12, 2023
read_copynumber_ascat.Rd		read_copynumber_ascat.Rd	Added read_copynumber_ascat	Aug 23, 2021
read_copynumber_seqz.Rd		read_copynumber_seqz.Rd	❇️ Add read_copynumber_seqz #237	Jun 22, 2020
read_maf.Rd		read_maf.Rd	retry submit	Jul 7, 2023
read_sv_as_rs.Rd		read_sv_as_rs.Rd	Removed package 'copynumber' from suggests filed.	Mar 29, 2023
read_vcf.Rd		read_vcf.Rd	Update read_vcf.Rd	Dec 5, 2023
read_xena_variants.Rd		read_xena_variants.Rd	Fix CRAN note	Jan 8, 2021
report_bootstrap_p_value.Rd		report_bootstrap_p_value.Rd	Add feature to report bootstrap p value	Apr 28, 2020
same_size_clustering.Rd		same_size_clustering.Rd	update docs	Mar 27, 2023
scoring.Rd		scoring.Rd	update docs	May 11, 2024
show_catalogue.Rd		show_catalogue.Rd	Move plotting to donttest block	Jul 7, 2023
show_cn_circos.Rd		show_cn_circos.Rd	set up t2t support	Dec 12, 2023
show_cn_components.Rd		show_cn_components.Rd	update doc	Mar 15, 2023
show_cn_distribution.Rd		show_cn_distribution.Rd	Try roxytest #115	Mar 13, 2020
show_cn_features.Rd		show_cn_features.Rd	update doc	Mar 15, 2023
show_cn_freq_circos.Rd		show_cn_freq_circos.Rd	set up t2t support	Dec 12, 2023
show_cn_group_profile.Rd		show_cn_group_profile.Rd	set up t2t support	Dec 12, 2023
show_cn_profile.Rd		show_cn_profile.Rd	set up t2t support	Dec 12, 2023
show_cor.Rd		show_cor.Rd	Update Rd	Nov 18, 2020
show_cosmic.Rd		show_cosmic.Rd	Close #288	Sep 30, 2020
show_cosmic_sig_profile.Rd		show_cosmic_sig_profile.Rd	Move plotting to donttest block	Jul 7, 2023
show_group_comparison.Rd		show_group_comparison.Rd	Move plotting to donttest block	Jul 7, 2023
show_group_distribution.Rd		show_group_distribution.Rd	Move plotting to donttest block	Jul 7, 2023
show_group_enrichment.Rd		show_group_enrichment.Rd	Fix bug & Added cluster_col to show_group_enrichment().	Mar 13, 2024
show_group_mapping.Rd		show_group_mapping.Rd	Move plotting to donttest block	Jul 7, 2023
show_groups.Rd		show_groups.Rd	🆕 Add show_groups	May 26, 2020
show_sig_bootstrap.Rd		show_sig_bootstrap.Rd	Try fixing action test	Nov 21, 2020
show_sig_consensusmap.Rd		show_sig_consensusmap.Rd	🐝 try fixing CRAN check doc warning again	Jun 17, 2020
show_sig_exposure.Rd		show_sig_exposure.Rd	Move plotting to donttest block	Jul 7, 2023
show_sig_feature_corrplot.Rd		show_sig_feature_corrplot.Rd	Move plotting to donttest block	Jul 7, 2023
show_sig_fit.Rd		show_sig_fit.Rd	Try fixing CRAN check failures	Aug 26, 2020
show_sig_profile.Rd		show_sig_profile.Rd	Move plotting to donttest block	Jul 7, 2023
show_sig_profile_heatmap.Rd		show_sig_profile_heatmap.Rd	Move plotting to donttest block	Jul 7, 2023
show_sig_profile_loop.Rd		show_sig_profile_loop.Rd	Move plotting to donttest block	Jul 7, 2023
sig_auto_extract.Rd		sig_auto_extract.Rd	update docs	May 11, 2024
sig_convert.Rd		sig_convert.Rd	Move plotting to donttest block	Jul 7, 2023
sig_estimate.Rd		sig_estimate.Rd	remove tally_M	Sep 5, 2021
sig_extract.Rd		sig_extract.Rd	remove tally_M	Sep 5, 2021
sig_fit.Rd		sig_fit.Rd	update docs	May 11, 2024
sig_fit_bootstrap.Rd		sig_fit_bootstrap.Rd	update docs	May 11, 2024
sig_fit_bootstrap_batch.Rd		sig_fit_bootstrap_batch.Rd	update docs	May 11, 2024
sig_operation.Rd		sig_operation.Rd	update doc	Dec 15, 2020
sig_tally.Rd		sig_tally.Rd	update docs	Mar 27, 2023
sig_unify_extract.Rd		sig_unify_extract.Rd	remove tally_M	Sep 5, 2021
sigminer-package.Rd		sigminer-package.Rd	Fix bug & Added cluster_col to show_group_enrichment().	Mar 13, 2024
sigprofiler.Rd		sigprofiler.Rd	set up t2t support	Dec 12, 2023
simulated_catalogs.Rd		simulated_catalogs.Rd	Fix CRAN note	Jan 8, 2021
simulation.Rd		simulation.Rd	Store best practice work	Nov 15, 2020
subset.CopyNumber.Rd		subset.CopyNumber.Rd	Rewrite from read to derive	Sep 9, 2019
tidyeval.Rd		tidyeval.Rd	fix url issue	Aug 9, 2022
transcript.T2T.Rd		transcript.T2T.Rd	update docs and change doc site deploy way	Dec 12, 2023
transcript.hg19.Rd		transcript.hg19.Rd	Add datasets	Apr 17, 2020
transcript.hg38.Rd		transcript.hg38.Rd	Add datasets	Apr 17, 2020
transcript.mm10.Rd		transcript.mm10.Rd	bump version	Apr 29, 2021
transcript.mm9.Rd		transcript.mm9.Rd	update doc	May 18, 2021
transform_seg_table.Rd		transform_seg_table.Rd	set up t2t support	Dec 12, 2023
use_color_style.Rd		use_color_style.Rd	Incluse RS as a member of sigminer, close #300	Oct 20, 2020
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