sigminer - v2.3.0

• Supported human T2T genome and corresponding annotation data.
• Updated COSMIC database to v3.4. SV and RNA-SBS signatures are included.

r get_sig_db("latest_RNA-SBS_GRCh37") get_sig_db("latest_SV_GRCh38")

• Fixed a bug in generating matrix for variation categories with strand bias due to problematic counting. (#445)

- R
Published by ShixiangWang about 2 years ago

sigminer - v2.2.2

Removed sigflow - sigprofiler as the default due to the install issue. If you wanna use the sigprofiler, please previous version or install it with interactive mode.

- R
Published by ShixiangWang over 2 years ago

sigminer - Release v2.2.1

sigminer 2.2.1

• Fixed the error in generating SBS matrix when only one sample input (#432).

sigminer 2.2.0

• Removed package 'copynumber' from suggests filed.
• Supported Ziyu Tao et al approach for copy number segment classification.
• Supported ce11 genome in read_vcf().
• Added read_maf_minimal() to support a minimal MAF-like data as input.

- R
Published by ShixiangWang almost 3 years ago

sigminer - Release v2.1.3

sigminer 2.1.3

• Fixed error in extracting invalid regions (#396, thanks to @KirsieMin).

sigminer 2.1.2

• Enhanced the read_copynumber_seqz() to include minor copy number. (Thanks to yancey)
• Added input range check in sig_estimate(). (#391)

sigminer 2.1.1

• Expanded output_* function by adding option sig_db.
• Fixed the error using sigminer::get_genome_annotation() before loading it.
• Fixed the bug the get_pLOH_score() return nothing for sample without LOH.

- R
Published by ShixiangWang almost 4 years ago

sigminer - Release 2.1.0

• Added sig_unify_extract() as an unified signature extractor.
• Fixed error showing copy number reference signature profile for CNS_TCGA database.

- R
Published by ShixiangWang over 4 years ago

sigminer - Release 2.0.5

• Impl y_limits option in show_sig_profile() (#381).
• Added function get_pLOH_score() for representing the genome that displayed LOH.
• Added function read_copynumber_ascat() for reading ASCAT result ASCAT object in .rds format.
• Added function get_intersect_size() for getting overlap size between intervals.
• Added option to get_Aneuploidy_score() to remove short arms of chr13/14/15/21/22 from calculation.

- R
Published by ShixiangWang over 4 years ago

sigminer - Release 2.0.4

• Implemented Cohen-Sharir method-like Aneuploidy Score.
• Enhanced error handling in show_sig_feature_corrplot() (#376).
• Fixed INDEL classification.
• Fixed end position determination in read_vcf().
• Updated INDEL adjustment.
• Included TCGA copy number signatures from SigProfiler.
• Updated docs.

- R
Published by ShixiangWang over 4 years ago

sigminer - Release 2.0.1

• Supported mm9 genome build.
• Removed FTP link as CRAN suggested (#359).
• Updated README.

- R
Published by ShixiangWang almost 5 years ago

sigminer - Release 2.0.0

BUG REPORTS

• Fixed the SigProfiler installation error due to Python version in conda environment.
• Fixed classification bug due to repeated function name call_component.
• Fixed the bug when read_vcf() with ## commented VCF files.

ENHANCEMENTS

• Added support for latest COSMIC v3.2 as reference signatures. You can obtain them by

r for (i in c("latest_SBS_GRCh37", "latest_DBS_GRCh37", "latest_ID_GRCh37", "latest_SBS_GRCh38", "latest_DBS_GRCh38", "latest_SBS_mm9", "latest_DBS_mm9", "latest_SBS_mm10", "latest_DBS_mm10", "latest_SBS_rn6", "latest_DBS_rn6")) { message(i) get_sig_db(i) }

• Updated keep_only_pass to FALSE at default.
• Added RSS and unexplained variance calculation in get_sig_rec_similarity().
• Added data check and filter in output_tally() and show_catalogue().
• Enhanced show_group_enrichment() (#353) & added a new option to cluster rows.
• Removed unnecessary CN classifications code in recent development.

NEW FUNCTIONS

DEPRECATED

• Dropped copy number "M"" method to avoid misguiding user to use/read wrong signature profile and keep code simple.

- R
Published by ShixiangWang almost 5 years ago

sigminer - V2 预览版

这是一个预览版本，目前看来基本可以发布，但需要对 sigflow 进行相关测试。

- R
Published by ShixiangWang almost 5 years ago

sigminer - Release v1.2.5

sigminer 1.2.5

BUG REPORTS

ENHANCEMENTS

• Modified the default visualization of bp_show_survey().
• Enhanced torch check.

NEW FUNCTIONS

• read_sv_as_rs() and sig_tally.RS() for simplified genome rearrangement classification matrix generation (experimental).

DEPRECATED

sigminer 1.2.4

BUG REPORTS

• Fixed the assign problem about match pair in bp_extract_signatures() with lpSolve package instead of using my problematic code.

ENHANCEMENTS

• Supported mm10 in read_vcf().
• Removed large data files and store them in Zenodo to reduce package size.
• Added cores check.
• Upgraded SP to v1.1.0 (need test).
• Tried installing Torch before SP (need test).

NEW FUNCTIONS

DEPRECATED

- R
Published by ShixiangWang about 5 years ago

sigminer - Release v1.2.2

BUG REPORTS

• Fixed bug in silhouette calculation in bp_extract_signatures() (#332). PAY ATTENTION: this may affect results.
• Fixed bug using custom signature name in show_sig_profile_loop().

ENHANCEMENTS

• Update SigProfilerExtractor to v1.1.0 (not tested).
• Subset signatures to plot is available by sig_names option.
• sigminer is available in bioconda channel: https://anaconda.org/bioconda/r-sigminer/
• Updated ms strategy in sig_auto_extract() by assigning each signature to its best matched reference signatures.
• Added get_shannon_diversity_index() to get diversity index for signatures (#333).
• Added new method "S" (from Steele et al. 2019) for tallying copy number data (#329).
• Included new (RS) reference signatures (related to #331).
• Updated the internal code for getting relative activity in get_sig_exposure().

NEW FUNCTIONS

• bp_get_clustered_sigs() to get clustered mean signatures.

DEPRECATED

- R
Published by ShixiangWang about 5 years ago

sigminer - Release v1.2.1

- R
Published by ShixiangWang about 5 years ago

sigminer - Release v1.2.0

BUG REPORTS

ENHANCEMENTS

• A new option cut_p_value is added to show_group_enrichment() to cut continous p values as binned regions.
• A Python backend for sig_extract() is provided.
• User now can directly use sig_extract() and sig_auto_extract() instead of loading NMF package firstly.
• Added benchmark results for different extraction approaches in README.
• The threshold for auto_reduce in sig_fit() is modified from 0.99 to 0.95 and similarity update threshold updated from >0 to >=0.01.
• Removed pConstant option from sig_extract() and sig_estimate(). Now a auto-check function is created for avoiding the error from NMF package due to no contribution of a component in all samples.

NEW FUNCTIONS

• bp_show_survey2() to plot a simplified version for signature number survey (#330).
• read_xena_variants() to read variant data from UCSC Xena as a MAF object for signature analysis.
• get_sig_rec_similarity() for getting reconstructed profile similarity for Signature object (#293).
• Added functions start with bp_ which are combined to provide a best practice for extracting signatures in cancer researches. See more details, run ?bp in your R console.

DEPRECATED

- R
Published by ShixiangWang about 5 years ago

sigminer - Release v1.1.0

• Added data simulation.
• Suppressed future warnings.
• Fixed p value calculation in bootstrap analysis.
• Fixed typo in show_cor(), thanks to @Miachol.
• Added y_tr option in show_sig_profile() to transform y axis values.
• Optimized default behavior of read_copynumber().
  • Support LOH records when user input minor allele copy number.
  • Set complement = FALSE as default.
  • Free dependencies between option use_all and complement.
• Added visualization support for genome rearrangement signatures (#300).
• Added four database for reference signatures from https://doi.org/10.1038/s43018-020-0027-5 (#299).
• Added new measure 'CV' for show_sig_bootstrap() (#298).
• Added group_enrichment() and show_group_enrichment() (#277).
• Optimized signature profile visualization (#295).
• Updated ?sigminer documentation.
• Added ms strategy to select optimal solution by maximizing cosine similarity to reference signatures.
• Added same_size_clustering() for same size clustering.
• Added show_cosmic() to support reading COSMIC signatures in web browser (#288).
• Changed argument rel_threshold behavior in sig_fit() and get_sig_exposure(). Made them more consistent and allowed un-assigned signature contribution (#285).
• Updated all COSMIC signatures to v3.1 and their aetiologies (#287).

- R
Published by ShixiangWang over 5 years ago

sigminer - Release v1.0.19

• Added more specific reference signatures from SigProfiler, e.g. SBS_mm9.
• Supported data.frame as input object for sig in get_sig_similarity() and sig_fit().
• Modified g_label option in show_group_distribution() to better control group names.
• Added test option and variable checking in show_cor().
• Updated output_sig() to output signature exposure distribution (#280).
• Added show_cor() for general association analysis.
• Added options in show_group_distribution() to control segments.

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.18

• Fixed bugs when outputing only 1 signatures (related to https://github.com/ShixiangWang/sigflow/issues/17).
• Fixed label inverse bug in add_labels(), thanks to TaoTao for reporting.

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.17

• Handled , seperated indices in showcosmicsignatures.
• Added option set_order in get_sig_similarity() (#274).
• Outputed more stats information in output_sig().
• Fixed default y axis title in show_sig_bootstrap_error(), now it is "Reconstruction error (L2 norm)"

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.16

• Added auto_reduce option in sig_fit* functions to improve signature fitting.
• Return cosine similarity for sample profile in sig_fit().
• Set default strategy in sig_auto_extract() to 'optimal'.
• Supported search reference signature index in get_sig_cancer_type_index().
• Outputed legacy COSMIC similarity for SBS signatures.
• Added new option in sigprofiler_extract() to reduce failure in when refit is enabled.
• Outputed both relative and absolute signature exposure in output_sig().
• Updated background color in show_group_distribution().
• Modified the default theme for signature profile in COSMIC style.
• Updated the copy number classification method.

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.15

• Handle NULL catalogue.
• Supported ordering the signatures for results from SigProfiler.
• Supported importing refit results from SigProfiler.
• Set optimize option in sig_extract() and sig_auto_extract().

- R
Published by ShixiangWang over 5 years ago

sigminer - 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().

- R
Published by ShixiangWang over 5 years ago

sigminer - 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.

- R
Published by ShixiangWang over 5 years ago

sigminer - 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.

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.11

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

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.10

支持 sigprofiler v1.0.15

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.9

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

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.8.1

Modify the cutoff for longer segments.

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.8

- R
Published by ShixiangWang over 5 years ago

sigminer - v1.0.7

- R
Published by ShixiangWang over 5 years ago

sigminer - 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 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.

- R
Published by ShixiangWang over 5 years ago

sigminer - Sigminer v1.0.4

- R
Published by ShixiangWang almost 6 years ago

sigminer - v0.1.5

sigminer v0.1.5

• update introduction for package sigminer
• fix text problem provided by CRAN check team
• add sig_get_similarity function
• add toy datasets & update examples
• fix typo in sig_assign_samples
• export read_maf
• update README

sigminer v0.1.4

• add examples for all exported functions

sigminer v0.1.3

• add sig_summarize_subtypes function for summarize subtype data
• add draw_subtypes_comparison function for plotting summarized data from sig_summarize_subtypes function

sigminer v0.1.2

• add sig_get_correlation function
• add draw_sig_corrplot function

sigminer v0.1.1

• add subset.CopyNumber() for subset CopyNumber object
• add genome_measure slot for CopyNumber object

sigminer v0.1.0

• Added a NEWS.md file to track changes to the package.
• Finish basic functions, including
  • read data
  • prepare data
  • estimate signature number
  • extract signatures
  • plot copy number profile
  • plot signature profile
  • plot signature activity
  • ...

- R
Published by ShixiangWang about 7 years ago

sigminer - v0.1.3

see news.md

- R
Published by ShixiangWang about 7 years ago

sigminer - sigminer v0.1.1

• add subset.CopyNumber() for subset CopyNumber object
• add genome_measure slot for CopyNumber object

- R
Published by ShixiangWang about 7 years ago

sigminer - sigminer v0.1.0

• Added a NEWS.md file to track changes to the package.
• Finish basic functions, including
  • read data
  • prepare data
  • estimate signature number
  • extract signatures
  • plot copy number profile
  • plot signature profile
  • plot signature activity
  • ...

- R
Published by ShixiangWang about 7 years ago