NEWS.md

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

grandR 0.2.6

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

grandR 0.2.5

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()

grandR 0.2.3

Smaller updates

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

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 0.2.2

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

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

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

grandR documentation built on April 4, 2025, 2:27 a.m.