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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: | 0.2.5 |
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: | 2024-02-15 |
DOI: | 10.32614/CRAN.package.grandR |
Author: | Florian Erhard [aut, cre], Teresa Rummel [ctb], Lygeri Sakellaridi [ctb], Kevin Berg [ctb] |
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 |
Package source: | grandR_0.2.5.tar.gz |
Windows binaries: | r-devel: grandR_0.2.5.zip, r-release: grandR_0.2.5.zip, r-oldrel: grandR_0.2.5.zip |
macOS binaries: | r-release (arm64): grandR_0.2.5.tgz, r-oldrel (arm64): grandR_0.2.5.tgz, r-release (x86_64): grandR_0.2.5.tgz, r-oldrel (x86_64): grandR_0.2.5.tgz |
Old sources: | grandR archive |
Please use the canonical form https://CRAN.R-project.org/package=grandR to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.