Change Log

The record of all notable changes to this project will be documented in this file.

v0.2

1 Oct 2020, first release.

v0.9.2

12 May 2021, build workflow and create documentation

v0.9.3

18 May 2021, bug fix, deal with more tumor types

v0.9.4

11 Jun 2021, bug fix, update Scanpy to v1.7.2, deal with the correlation between predicted cell fractions of each cell type and mean gene expression of corresponding marker genes

v0.9.5

2 Jul 2021, typo fix, update Scanpy to v1.8.0 & update seaborn to v0.11.1

v0.9.6

7 Jul 2021, typo fix, check if Cancer Cells existed and update bbknn to v1.5.1

v0.9.6.1

16 Jul 2021, set total_cell_number to 100 and n_base to 3 when simulating bulk cell data for better keeping cell type diversity

v0.9.7

13 Sep 2021

  • Filtering single cell data of CD4 T and CD8 T cells by the ratio of marker genes

  • Updating marker gene list and re-annotating sub-clustering based on dot-plot figure of each single cell dataset

v0.9.8

19 Nov 2021

  • Building the whole workflow in one file

  • Recording main parameters and running logs

v1.0.2 (bioRxiv)

2 Jun 2023

  • Update documentation

v1.1.0

1 Oct 2023

  • Update the workflow to contain the following parameters:

    • alpha_total_rna_coefficient: the coefficient of total RNA for each cell type during the simulation of bulk RNA-seq data

    • cell_type2subtypes: the dictionary of cell types and their subtypes

  • Update the DNN model to include pathway profiles

  • Update the documentation

v1.2.0

16 Jan 2024

  • Add GEP-level filtering in the PCA space of TCGA samples

  • Add Dirichlet distribution to simulate the cellular proportions of bulk RNA-seq data

v1.2.2 (revision)

3 Feb 2024

  • Update the documentation

v1.3.1 (revision)

13 Jul 2024

  • Update Figure 1ab

  • Update workflow and plot functions during the revision

v1.3.2 (revision)

15 Sep 2024

  • Update documentation