Changelog

Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Version 0.0.4#

News#

Features#

  • Add gridsize parameter to dotools_py.pl.density to control the number of points calculated in each dimension.

  • Add spatial related functions such as do.io.read_visium, do.dt.example_visium,

  • Rename do.pp.sctransform_normalize to do.pp.pearson_residuals_normalize allowing python and r backends.

  • Improve do.pl.slides allowing to plot one or multiple slides.

  • Allow basic quality control of visium 10x data in dotools_py.pp.importer_py and dotools_py.pp.quality_control.

  • Add extra functions to do.utility and do.get

  • Add do.tl.run_seurat_integration allowing both python (experimental) and r backend

  • The behavior of logcounts changed for do.pl.barplot() use estimator instead to adapt the calculation.

  • Add logmean to do.get.mean_expr() to control if the mean or log-transformed mean is returned

Bug Fixes#

  • Fix Bug in dotools_py.pl.density related to axes ticks, colorbar and multiple feature plotting.

  • Fix Bugs in the dotools_py.pp module

  • Fix typo in the name of the function dotools_py.pl.split_embedding

  • Fix Bug in default matplotlib settings

  • Fix deprecation bug in SCTransform

  • Internal restructure.

Documentation#

  • Update scRNA-seq tutorial

  • Add Visium tutorial

  • Update citation and README

Version 0.0.3 2026-01-30#

Features#

  • Add dotools_py.pl.heatmap_foldchange to visualize log2foldchanges between groups across conditions.

  • Add io module for reading/writing. dotools_py.utility.read_rds and dotools_py.utility.save_rds have been moved to this module.

  • Make internal functions in dotools_py.pp and dotools_py.tl public.

  • Add dotools_py.get.layer_swap to swap layers.

  • Add dotools_py.settings.set_kernel_logger and :func:dotools_py.settings.toggle_kernel_logger to record the kernel history.

  • Add dotools_py.bm module that contain metrics for the evaluation of quality control steps.

  • Add dotools_py.pl.density to visualize density of features in embeddings.

  • Add random_state parameters to the methods.

  • Add dotools_py.utlity.create_report

  • Add dotools_py.tl.DGEAnalysis, a class with DGE analysis methods.

  • Add dotools_py.pl.ridgeplot

Bug fixes#

  • Fix Bug in dotools_py.pl.barplot, dotools_py.pl.boxplot and dotools_py.pl.violinplot where the legends were not correctly display when hue was set but hue_order was not set.

  • Embedding plots will be saved using a vector_friendly (scatter plots will use png backend even when exporting as PDF or SVG).

  • Internal bug fixes in several other methods

  • Harmony runs through the pytorch implementation.

Version 0.0.2 2025-11-25#

Correction of bugs and update parameters naming for consistency across functions.

Version 0.0.1 2025-10-23#

Pre-release of DoTools, a convenient and user-friendly package to streamline common workflows in single-cell RNA sequencing data analysis using the scverse ecosystem.