v1.0.14

• Supported signature index separated by , in sig_fit() and sig_fit_bootstrap* functions.
• Added output_* functions from sigflow.
• Enhanced DBS search and error handling in sig_tally().
• Added option highlight_genes in show_cn_group_profile() to show gene labels.
• Added get_sig_cancer_type_index() to get reference signature index.
• Added show_group_distribution() to show group distribution.
• Added options in show_cn_profile() to show specified ranges and add copy number value labels.
• Used package nnls instead of pracma for NNLS implementation in sig_fit().

v1.0.13

• Supported BSgenome.Hsapiens.1000genomes.hs37d5 in sig_tally().
• Remove changing MT to M in mutation data.
• Fixed bug in extract numeric signature names and signature orderings in show_sig_exposure().
• Added letter_colors as an unexported discrete palette.

v1.0.12

• Added transform_seg_table().
• Added show_cn_group_profile().
• Added show_cn_freq_circos().
• sig_orders option in show_sig_profile() function now can select and order signatures to plot.
• Added show_sig_profile_loop() for better signature profile visualization.

v1.0.11

• Added option to control the SigProfilerExtractor to avoid issue in docker image build.

v1.0.10

支持 sigprofiler v1.0.15

v1.0.9

• Tried to speed up joining adjacent segments in read_copynumber(), got 200% improvement.

v1.0.8.1

Modify the cutoff for longer segments.

v1.0.8

:bug: Fix bug caused by unsorted input data

v1.0.7

:+1: speed up copy number annotation, close #230

v1.0.6

sigminer 1.0.6

• lsei package was removed from CRAN, here I reset default method to 'QP' and tried best to keep the LS usage in sigminer (#189).
• Made consistent copy number labels in show_sig_profile() and added input checking for this function.
• Fixed unconsistent bootstrap when use furrr, solution is from futureverse/furrr#107.
• Properly handled null-count sample in sig_fit() for methods QP and SA.
• Supported boxplot or violin in show_sig_fit() and show_sig_bootstrap_* functions.
• Added job mode for sig_fit_bootstrap_batch for more useful in practice.
• Added show_groups() to show the signature contribution in each group from get_groups().
• Expanded clustering in get_groups() to result of sig_fit().
• Properly handled null-count samples in sig_fit_bootstrap_batch().
• Added strand bias labeling for INDEL.
• Added COSMIC TSB signatures.

sigminer 1.0.5

• Exported APOBEC result when the mode is 'ALL' in sig_tally().
• Added batch bootstrap analysis feature (#158).
• Supported all common signature plotting.
• Added strand feature to signature profile.

sigminer 1.0.4

• Added profile plot for DBS and INDEL.
• Fixed error for signature extraction in mode 'DBS' or 'ID'.
• Fixed method 'M' for CN tally cannot work when cores > 1 (#161).

sigminer 1.0.3

• Added multiple methods for sig_fit().
• Added feature sig_fit_bootstrap() for bootstrap results.
• Added multiple classification method for SBS signature.
• Added strand bias enrichment analysis for SBS signature.
• Moved multiple packages from field Imports to Suggests.
• Added feature report_bootstrap_p_value() to report p values.
• Added common DBS and ID signature.
• Updated citation.

sigminer 1.0.2

• Added merged transcript info for hg19 and hg38 build, this is availabe by data().
• Added gene info for hg19 and hg38 build to extdata directory.

sigminer 1.0.1

• Removed fuzzyjoin package from dependency.
• Moved ggalluvial package to field suggsets.

sigminer 1.0.0

All users, this is a break-through version of sigminer,
most of functions have been modified, more features are implemented.
Please read the reference list to see the function groups and their
functionalities.

Please read the vignette for usage.

I Hope it helps your research work and makes a new contribution
to the scientific community.