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 Documentation: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=grandR to link to this page.
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