Changes in version 0.2.7 (2026-01-14)                  

Major updates

  - Removed dependency to monocle (which caused problems on the newest
    cran build)
  - Added wilcoxon test (optionally via presto) for differential gene
    expression

Smaller updates

  - More useful parameter name count.as.integer for GetTable, GetMatrix
    and GetData
  - Expanded code for estimation in the mixture model
  - Removed the ComputeAbsolute function
  - Reading llr and shape matrices of Grand3 output

                 Changes in version 0.2.6 (2025-01-22)                  

Major updates

  - Can now read and process Grand3 output
  - Hetseq vignette

Smaller updates

  - Keep parameter for FilterGenes now allows not only logical vectors
  - Total expression computation
  - n.obs in PlotScatter
  - Merge can now work genewise

Shiny improvement

  - Plotting function can now either implement the arguments highlight
    and label or not
  - Bug fixes with spaces in names of plots
  - Pdfs in subfolders are now included in the reports menu
  - Floating windows
  - Improved handling of highlighted genes

                 Changes in version 0.2.5 (2024-02-15)                  

Shiny improvement

  - If there are global plots, there is now an additional page showing
    the highlighted genes
  - Defer now allows to specify desired figure width and height
  - Fixed bug that caused all global plots to be executed before
    rendering the main table
  - Html files that are in the same ordner are linked (under menu
    Reports)
  - Now multiple tables can be provided (as named list)
  - Additiona, static plots can be shown in floating windows

Smaller updates

  - fixed subsetting of grandR to only a single column
  - improved handling of factors in coldata during merging
  - Updated ReadGRAND3 to most recent Grand3 version (mode output)
  - Improved ComputeColumnStatistics (percentage calculations)
  - Differential gene expression analysis for a subset of the genes
    (including normalization to only those genes)
  - FormatCorrelation can add RMSDs
  - Statistics for Plot4sUDropout()

                        Changes in version 0.2.3                        

Smaller updates

  - compute.M for LFC
  - size factors to normalize Pairwise, LFC and PairwiseDESeq2

                 Changes in version 0.2.2 (2023-04-20)                  

This is the release of grandR including improvements for the submission
of the grand-Correct preprint

Major updates

  - Enable simulation with non-constant rates
  - 4sU dropout plots and grand-Correct functionality

Smaller updates

  - Fixed a bug that caused warning messages after loading files.

This is the release of grandR including improvements for the submission
of the grand-Correct preprint

Major updates

  - Enable simulation with non-constant rates
  - 4sU dropout plots and grand-Correct functionality

Smaller updates

  - Fixed a bug that caused warning messages after loading files.

                 Changes in version 0.2.1 (2023-02-27)                  

This is the release of grandR including improvements for the revised
version of the manuscript.

Major updates

  - Enabled interface with Seurat
  - Implemented estimation for pulse-chase experiments
  - New vignettes for single cell data and pulse-chase data
  - 4sU dropout plots
  - Highlighting genes in the shiny web interface
  - Cheatsheet

Smaller updates

  - Compute BIC values for a list of models per gene and save it as an
    analysis table
  - Additional parameters to PlotScatter
  - Updated all calls to aes_string by tidy evaluation (for ggplot2 3.0
    compatibility)
  - Semantics for concentration fields
  - Fixed issues when merging two data sets that were independently
    processed and have gene name dublettes
  - FitKineticsGeneNtr now also computes residuals

                 Changes in version 0.2.0 (2022-09-20)                  

This is the first release of grandR.

Available functionality

  - Functions for loading GRAND-SLAM data
  - Function for preprocessing
  - Functions for kinetic modeling of progressive labeling time courses
  - Functions to infer synthesis and half-lives from snapshot data
  - Many helper functions (plotting, read simulation, etc.)
  - Web-interface via shiny