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 [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 |