Release Notes

Version 0.2.1 February 15, 2023

This version includes:

  • Add treated mice data.

  • Fix linting bug.

Version 0.2.0 January 27, 2023

This version includes:

  • Add bWES data.

  • Add bWTS data.

  • Add scRNA data.

  • Fix the bug of CI.

Version 0.1.1 December 28, 2022

This version includes:

  • Fix the bug of CI.

Version 0.0.21 April 22, 2022

This version includes:

  • Fix some bugs.

  • Improve the documentations.

Version 0.0.20 November 22, 2021

This version includes:

  • Add multi-threaded ScisTree.

  • Update the documentations.

Version 0.0.19 October 18, 2021

This version includes:

  • Add GRMT and SPhyR as new solvers.

  • Update the consensus to new algorithm.

  • Fix some bugs.

Version 0.0.18 October 13, 2021

This version includes:

  • Add Robinson-Foulds metric into the score module.

  • Fix the installation bug.

Version 0.0.17 September 29, 2021

This version includes:

  • Fix the installation bug.

Version 0.0.16 September 27, 2021

This version includes:

  • Add CASet and DISC for scoring two trees.

  • Add mp3 for scoring two trees.

  • Update dataset.

  • Add more tests.

  • Fix some bugs and typos.

Version 0.0.15 September 24, 2021

This version includes:

  • Add consensus Day algorithm.

  • Some bug fixes and typos.

  • Add more tests.

Version 0.0.14 September 5, 2021

This version includes:

  • Add more tests.

Version 0.0.13 September 2, 2021

This version includes:

  • Lots of bug fixes and typos.

  • Add more tests.

  • Add more datasets.

Version 0.0.12 July 7, 2021

This version includes:

  • Fix some bugs and typos.

  • Add partition function command to the CLI.

Version 0.0.11 July 4, 2021

This version includes:

  • Fix some typos.

  • Fix some bugs.

  • Fix SCITE cythonizing issue.

Version 0.0.10 July 3, 2021

This version includes:

  • Fix some typos.

  • Fix some bugs.

Version 0.0.9 June 17, 2021

This version includes:

  • Fix some typos.

  • Add flake8 support.

Version 0.0.8 June 12, 2021

This version includes:

  • Trisicell-Boost function.

  • A few more examples in the documentations.

Version 0.0.7 May 29, 2021

This version includes:

  • PhISCS with readcount model.

  • Cythonizing all the cpp files including SCITE, ScisTree and MLTD.

  • Fix some bugs and typos.

  • New datasets:

    • Leung et al., 2017 (colorectal cancer patient 1)

Version 0.0.6 May 25, 2021

This version includes:

  • Add Stochastic Block Models (SBM) for sparse matrices.

  • New datasets:

    • Hou et al., 2012 (myeloproliferative neoplasm).

    • Xu et al., 2012 (renal cell carcinoma).

    • Li et al., 2012 (muscle invasive bladder).

    • Wang et al., 2014 (oestrogen-receptor-positive breast cancer).

    • Wang et al., 2014 (triple-negative breast cancer).

    • Gawad et al., 2014 (acute lymphocytic leukemia patient 2).

Version 0.0.5 May 4, 2021

This version includes:

  • Writing intermediate file in /tmp directory.

  • Fix some bugs.

Version 0.0.4 April 17, 2021

This version includes:

  • Add copy number tool.

  • Fix some bugs.

Version 0.0.3 April 8, 2021

This version includes:

  • Consensus tree builder with CLI command.

  • Some new utility functions such as converting a tree fo conflict-free matrix.

  • Bifiltering ILP code for selecting the maximal informed submatrix.

Version 0.0.2 March 29, 2021

Second beta release of Trisicell. This version includes:

  • Solvers including (SCITE, PhISCS and etc).

  • Preprocessing of the readcount matrices.

  • Partition function estimation.

  • Mutation calling commands for genotyping single-cell RNA data.

  • Set of genotype noisy/solution datasets.

  • Functions for comparing two clonal trees.

  • Functions for plotting clonal/dendrogram trees.

Version 0.0.1 March 25, 2021

First beta release of Trisicell.