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Recent Releases of sigprofilermatrixgenerator

sigprofilermatrixgenerator - v1.3.5

What's Changed

  • Update README.md by @azhark2 in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/231
  • U71 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/232
  • v1.3.5 Updates by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/233

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.3.4...v1.3.5

- Python
Published by mdbarnesUCSD 7 months ago

sigprofilermatrixgenerator - v1.3.4

What's Changed

  • Fix context_counts by @PilarGallego in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/227
  • Development by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/230

New Contributors

  • @PilarGallego made their first contribution in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/227

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.3.3...v1.3.4

- Python
Published by mdbarnesUCSD 9 months ago

sigprofilermatrixgenerator - v1.3.3

What's Changed

  • Deprecate ICGC format support by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/223
  • Fix plot_type parameter for ID plotting by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/222
  • Development by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/224

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.3.2...v1.3.3

- Python
Published by mdbarnesUCSD 10 months ago

sigprofilermatrixgenerator - v1.3.2

What's Changed

  • Fix SV example file extensions. by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/217
  • Context distribution updates for rn7 and mm39 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/219
  • Development by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/220

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.3.1...v1.3.2

- Python
Published by mdbarnesUCSD 11 months ago

sigprofilermatrixgenerator - v1.3.1

What's Changed

  • Window index issue by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/214
  • Spm i213 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/215

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.3.0...v1.3.1

- Python
Published by mdbarnesUCSD 12 months ago

sigprofilermatrixgenerator - v1.3.0

What's Changed

  • Update README.md by @azhark2 in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/206
  • Update README to include rn7 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/208
  • Pandas2 up by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/210
  • Requires Pandas and Numpy >= 2.0.0 and Python >= 3.9

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.31...v1.3.0

- Python
Published by mdbarnesUCSD about 1 year ago

sigprofilermatrixgenerator - v1.2.31

What's Changed

  • I201 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/203

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.30...v1.2.31

- Python
Published by mdbarnesUCSD over 1 year ago

sigprofilermatrixgenerator - v1.2.30

What's Changed

  • Fixed the indel issue for exome by @MousumyCSE in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/200

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.29...v1.2.30

- Python
Published by mdbarnesUCSD over 1 year ago

sigprofilermatrixgenerator - v1.2.29

What's Changed

  • Sorting input exome by @MousumyCSE in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/197

New Contributors

  • @MousumyCSE made their first contribution in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/197

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.28...v1.2.29

- Python
Published by mdbarnesUCSD over 1 year ago

sigprofilermatrixgenerator - v1.2.28

What's Changed

  • Fix CI/CD badge by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/190
  • SV VCF by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/191

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.27...v1.2.28

- Python
Published by mdbarnesUCSD over 1 year ago

sigprofilermatrixgenerator - v1.2.27

What's Changed

  • Development by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/189

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.26...v1.2.27

- Python
Published by mdbarnesUCSD over 1 year ago

sigprofilermatrixgenerator - v1.2.26

What's Changed

  • Upgrade to v1.2.26 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/180

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.25...v1.2.26

- Python
Published by mdbarnesUCSD almost 2 years ago

sigprofilermatrixgenerator - v1.2.25

What's Changed

  • v1.2.25: Add rn7 and resolve custom install tsb_BED path issue by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/175

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.24...v1.2.25

- Python
Published by mdbarnesUCSD about 2 years ago

sigprofilermatrixgenerator - v1.2.24

What's Changed

  • Update v1.2.24: Fix ebv matrix generation by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/174

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.23...v1.2.24

- Python
Published by mdbarnesUCSD about 2 years ago

sigprofilermatrixgenerator - v1.2.23

What's Changed

Added to CLI: 1. SV matrix generator 2. CNV matrix generator

Additional changes: 1. Added Dockerfile 2. Modified reference_paths to accept a volume

  • Upgrade to v1.2.23 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/173

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.22...v1.2.23

- Python
Published by mdbarnesUCSD about 2 years ago

sigprofilermatrixgenerator - v1.2.22

What's Changed

  • v1.2.22: CLI installs reference genomes using the ReferenceGenomeMana… by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/170

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.21...v1.2.22

- Python
Published by mdbarnesUCSD about 2 years ago

sigprofilermatrixgenerator - v1.2.21

What's Changed

  • Add ReferenceGenomeManager that: by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/169
  • Remove benchmark script that was run in site-packages after a reference genome was installed

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.20...v1.2.21

- Python
Published by mdbarnesUCSD about 2 years ago

sigprofilermatrixgenerator - v1.2.20

What's Changed

  • I161 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/163

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.19...v1.2.20

- Python
Published by mdbarnesUCSD about 2 years ago

sigprofilermatrixgenerator - v1.2.19

What's Changed

  • Remove chdir by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/157

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.18...v1.2.19

- Python
Published by mdbarnesUCSD over 2 years ago

sigprofilermatrixgenerator - v.1.2.18

Release Notes for v1.2.18

Enhancements

  • New Command-Line Interface (CLI):

    • A new and intuitive CLI, SigProfilerMatrixGenerator_CLI.py, has been launched to facilitate user interactions.
    • This interface accommodates essential tasks such as install and matrix_generator.
    • Enhanced user control for saving/loading reference genomes with the addition of the volume parameter.

  • Testing Improvements:

    • Introduced additional tests to better validate the functionalities and ensure more reliable outcomes.

Additional Updates

  • File Naming Update: To resolve issues with CLI imports, SigProfilerMatrixGenerator.py has been renamed to MutationMatrixGenerator.py.

  • Documentation Refinement: The README has been revised to include the CLI updates.

  • Added a status badge to indicate the FTP server's uptime.

Limitations

  • CLI and CNV/SV Support: Please note that the current version of the CLI does not support CNV/SV functionalities. We are actively working on this and will provide updates in future releases.

- Python
Published by mdbarnesUCSD over 2 years ago

sigprofilermatrixgenerator - Version 1.2

Stable version after releasing a series of hotfixes for compatibility across the SigProfiler suite of tools along with the support for additional reference genomes, custom genome installations, and offline genome installations.

- Python
Published by ebergstr over 4 years ago

sigprofilermatrixgenerator - Version 1.1

Stable version after releasing a series of hotfixes for compatibility across the SigProfiler suite of tools.

- Python
Published by ebergstr about 6 years ago

sigprofilermatrixgenerator - release version 1.0

- Python
Published by ebergstr over 6 years ago