Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such experiments require specialized tools for primary processing such as GRAND-SLAM, (see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for downstream analyses. 'grandR' provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data.
Version: | 0.2.6 |
Depends: | R (≥ 3.5.0) |
Imports: | stats, Matrix, rlang, ggplot2, grDevices, patchwork, RCurl, plyr, parallel, reshape2, MASS, scales, cowplot, minpack.lm, lfc, labeling, methods, utils, numDeriv |
Suggests: | knitr, rmarkdown, circlize, Seurat, ComplexHeatmap, ggrepel, DESeq2, S4Vectors, data.table, clusterProfiler, biomaRt, msigdbr, fgsea, rclipboard, cubature, DT, shinyjs, shinyjqui, RColorBrewer, gsl, htmltools, matrixStats, monocle, VGAM, quantreg, graphics, shiny, ggrastr, viridisLite, deSolve |
Published: | 2025-01-22 |
DOI: | 10.32614/CRAN.package.grandR |
Author: | Florian Erhard |
Maintainer: | Florian Erhard <Florian.Erhard at informatik.uni-regensburg.de> |
BugReports: | https://github.com/erhard-lab/grandR/issues |
License: | Apache License (≥ 2) |
URL: | https://github.com/erhard-lab/grandR |
NeedsCompilation: | yes |
Citation: | grandR citation info |
Materials: | README NEWS |
CRAN checks: | grandR results |
Reference manual: | grandR.pdf |
Vignettes: |
Getting started (source, R code) |
Package source: | grandR_0.2.6.tar.gz |
Windows binaries: | r-devel: grandR_0.2.6.zip, r-release: grandR_0.2.6.zip, r-oldrel: grandR_0.2.6.zip |
macOS binaries: | r-devel (arm64): grandR_0.2.6.tgz, r-release (arm64): grandR_0.2.6.tgz, r-oldrel (arm64): grandR_0.2.6.tgz, r-devel (x86_64): grandR_0.2.6.tgz, r-release (x86_64): grandR_0.2.6.tgz, r-oldrel (x86_64): grandR_0.2.6.tgz |
Old sources: | grandR archive |
Reverse imports: | HetSeq |
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