sigminer 1.0.7

• Removed useless options in read_maf().
• Modify method ‘LS’ in sig_fit() to ‘NNLS’ and implement it with pracma package (#216).
• Made use_all option in read_copynumber() working correctly.
• Fixed potential problem raised by unordered copy number segments (#217).
• Fixed a typo, correct MRSE to RMSE.
• Added feature in show_sig_bootstrap_*() for plotting aggregated values.
• Fixed bug when use get_groups() for clustering.
• Fixed bug about using reference components from NatGen 2018 paper.
• Added option highlight_size for show_sig_bootstrap_*().
• Fixed bug about signature profile plotting for method ‘M’.

sigminer 1.0.6

• Added “scatter” in sig_fit() function to better visualize a few samples.
• Added “highlight” option.
• 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 https://github.com/DavisVaughan/furrr/issues/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.