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Changelog

Source: NEWS.md

grandR 0.2.2

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.

grandR 0.2.1

CRAN release: 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

grandR 0.2.0

CRAN release: 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