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.