Release for mSigHdp paper and 2 earlier papers

This release is used to generate benchmarking datasets in three papers:

(Under revision) Liu, M. et al. mSigHdp: hierarchical Dirichlet processes in mutational signature extraction.

(Published in Nature) Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020). https://doi.org/10.1038/s41586-020-1943-3

(Published in Scientific Reports) Wu, Y. et al. Accuracy of Mutational Signature Software on Correlated Signatures. Scientific Reports 12, 390 (2022). https://doi.org/10.1038/s41598-021-04207-6

NOTE: Please use this release instead of 1.1.0-release, as this release excludes unused signatures from "ground.truth.syn.sigs.csv" in each spectra dataset of Liu et al. (2022).

Release for Nature paper and SREP paper "Accuracy of Mutational Signature Software on Correlated Signatures"

This release is used to generate benchmarking datasets in two papers:

(Published in Nature) Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020). https://doi.org/10.1038/s41586-020-1943-3

(Accepted by Scientific Reports) Wu, Y. et al. Accuracy of Mutational Signature Software on Correlated Signatures

Please use this release instead of 1.0.5, as version 1.0.5 will fail test test-AddNoise.R after user upgrades one dependency package, PCAWG7. The new PCAWG7 package no more uses COSMIC v3.0 signatures as default signature set.

For benchmarking datasets in
Liu, M. et al. mSigHdp: hierarchical Dirichlet processes in mutational signature extraction
, please go to SynSigGen version 1.1.1+.

Old Release for SBS1-SBS5-Testing-Paper and Nature-Paper (Please use 1.0.6)

Simplified

• Simplified folder structure of SBS1-SBS5-correlated dataset,
  generated by CreateSBS1SBS5CorrelatedSyntheticData() -
  The files of synthetic datasets are under the dataset folders, and no more
  sp.sp folders.

The citation of Nature paper is listed below:

Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020). https://doi.org/10.1038/s41586-020-1943-3

The evaluation of signature extraction tools on SBS1-SBS5 datasets is currently accepted by Scientific Reports.

Please use release 1.0.6 instead of this release, as version 1.0.5 will fail test test-AddNoise.R after user upgrades one dependency package, PCAWG7. The new PCAWG7 package no more uses COSMIC v3.0 signatures as default signature set.

Last version generates SBS1-SBS5-correlated dataset with two-layer directory structure

Last version generates SBS1-SBS5-correlated dataset with two-layer directory structure:

• Name of dataset (e.g. S.0.1.Rsq.0.1)
• Folder sp.sp, means that two ground-truth signatures (SBS1 and SBS5) are from results of SigProfiler in (https://doi.org/10.1038/s41586-020-1943-3)
• Files of synthetic datasets.

The datasets for the SBS1-SBS5-correlated dataset paper should be generated by SynSigGen >= 1.0.5.

1.0.2.9005

Last stable release before submitting to CRAN.

1.0.2-release

1. Fixed SBS1-SBS5-correlated dataset generation code;
2. Added a test for SBS1-SBS5-correlated dataset generation.

v1.0.0

Initial stable release