CHANGELOG.md

In kharchenkolab/sccore: Core Utilities for Single-Cell RNA-Seq

Changelog

[1.0.5] - Feb 22 2024

• Remove /usr/lib linking in Makevars files
• Also remove -L"." -lpthread -lstdc++ -lm. Not necessary.

[1.0.4] - July 11 2023

• Added scale.center argument to dotPlot() to plot more intuitive and correct avg. expression levels.

[1.0.3] - March 12 2023

• Added checkPackageInstalled
• Added saveDeAsJson
• Bugfix for dotPlot
• Removed 'CXX_STD = CXX11' from the Makevars files, and removed 'SystemRequirements: C++11'

[1.0.2] - August 23 2022

Changed

• Fixed HTML5 validation issue requested by CRAN given R 4.2.0
• Removed a few if conditionals with 'class()'
• Set mc.allow.recursive=TRUE by default in 'plapply()'. (Explanation: "Somehow, without it multithreading is often disabled if progress=TRUE.Maybe, a bug in the library." https://github.com/kharchenkolab/sccore/commit/8566f3ded6b986592e683de1639649ea573cc36b)

[1.0.1] - December 11 2021

Changed

• Clarify roxygen2 documentation, palette arguments
• Fixed l.max parameter in smoothSignalOnGraph, added validation for graph connectivity
• extendMatrix doesn't drop dimensions anymore
• Fixed processing of mc.allow.recursive for n.cores=1 in plapply
• Export heatFilter()

[1.0.0] - October 7 2021

Changed

• The package does not rely on OpenMP anymore, all function use C++11 threads
• Better processing of corner cases in extendMatrix and smoothSignalOnGraph
• Fixed bug in val2ggcol with all color values <= 0: it now produces blue palette instead of read-blue
• Fixed extendMatrix() so that always subsets on col.names

[0.1.3] - May 4 2021

Added

• collapseCellsByType from Conos

Changed

• colSumByFactor now requires factor input and returns a named matrix
• Parallel cpp functions can now be accessed from other cpp packages by including sccore_par.hpp

[0.1.2] - February 19 2021

Added

• val2col function that translates values into colors
• added smoothSignalOnGraph function that re-implements graph filtering from the pygsp package
• Rcpp functions runTaskParallelFor, runTaskParallel and class ThreadProgress for parallel loops with progress bar using C++11 threads
• roxygen2 revisions

Changed

• plot.na can accept numeric values now. If plot.na passed a numeric value below 0, the NA symbols are plotted below the cells. Otherwise if values >=0, they're plotted above the cells.
• plapply now accepts fail.on.error parameter that is FALSE by default
• Small bug fixes
• plapply now uses pbmcapply

[0.1.1] - September 30 2020

kharchenkolab/sccore documentation built on Feb. 26, 2024, 12:41 a.m.