grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data (original) (raw)
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 |
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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 |
Documentation:
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