NEWS
grandR 0.2.7
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
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