grandr
R package for nucleotide conversion sequencing data analysis
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
13 of 18 committers (72.2%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.2%) to scientific vocabulary
Repository
R package for nucleotide conversion sequencing data analysis
Basic Info
Statistics
- Stars: 15
- Watchers: 1
- Forks: 3
- Open Issues: 5
- Releases: 5
Metadata Files
README.md
grandR 
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, 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.
Installation
grandR is available from CRAN. Install grandR using the following commands on the R console:
install.packages("grandR")
library(grandR)
You can also install the development version from github:
require("devtools")
devtools::install_github("erhard-lab/grandR")
library(grandR)
System Requirements
grandR should be compatible with Windows, Mac, and Linux operating systems, but we recommend using grandR on a Linux machine, where it has been extensively tested (Ubuntu 22.04). Due to restrictions of the parallel package, parallelization (SetParallel()) does not work under Windows. grandR runs on standard laptops (multi-core CPUs are recommended and memory requirements depend on the size of your data sets).
Installing it via install.packages or devtools::install_github will make sure that the following (standard) packages are available:
stats,Matrix,rlang,ggplot2,grDevices,patchwork,RCurl,plyr,parallel,reshape2,MASS,scales,cowplot,minpack.lm,lfc,labeling,methods,utils,numDeriv
Additional packages are optional and important for particular functions:
knitr, rmarkdown, circlize, Seurat, ComplexHeatmap, ggrepel, DESeq2, S4Vectors, data.table, clusterProfiler, biomaRt, msigdbr, fgsea, rclipboard, cubature, DT, RColorBrewer, gsl, htmltools, matrixStats, monocle, VGAM, quantreg, graphics, shiny, ggrastr, viridisLite
With all dependencies available, installation of grandR typically takes less than a minute.
Cheatsheet
How to get started
First have a look at the Getting started vignette.
Then, go through the Differential expression or the Kinetic modeling vignette, which provide a comprehensive walk-through of the two main settings of nucleotide conversion experiments.
There are also additional vignettes:
- Loading data and working with grandR objects: Learn more about programming with grandR
- Working with data matrices and analysis results: Learn more about how to retrieve data from grandR objects
- Plotting: Learn about the plotting helper functions and the shiny web-interface of grandR
- Pulse-chase: Learn how to fit pulse-chase data with grandR
- Single cell: Learn how to load and process single cell data with grandR
- 4sU dropout: Learn how to perform analysis of 4sU dropout
Owner
- Name: erhard-lab
- Login: erhard-lab
- Kind: organization
- Repositories: 4
- Profile: https://github.com/erhard-lab
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 1
- Watch event: 7
- Push event: 2
- Fork event: 1
Last Year
- Create event: 1
- Release event: 1
- Issues event: 1
- Watch event: 7
- Push event: 2
- Fork event: 1
Committers
Last synced: over 3 years ago
All Time
- Total Commits: 164
- Total Committers: 18
- Avg Commits per committer: 9.111
- Development Distribution Score (DDS): 0.384
Top Committers
| Name | Commits | |
|---|---|---|
| Florian Erhard | F****o@e****e | 101 |
| Teresa | t****7@g****m | 14 |
| Florian Erhard | f****o@e****e | 12 |
| Lygeri | L****i@E****l | 9 |
| Lygeri | L****i@w****e | 5 |
| Teresa | 9****l@u****m | 4 |
| Lygeri | L****i@w****e | 4 |
| Lygeri | L****i@w****e | 3 |
| florianerhard | F****d@u****e | 2 |
| Lygeri | L****i@w****e | 2 |
| Lygeri | L****i@w****e | 1 |
| Lygeri | L****i@w****e | 1 |
| Lygeri | L****i@w****e | 1 |
| Lygeri | L****i@w****e | 1 |
| Lygeri Sakellaridi | l****i@u****e | 1 |
| Lygeri | L****i@w****e | 1 |
| Lygeri | L****i@w****e | 1 |
| Lygeri | L****i@w****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 22
- Total pull requests: 0
- Average time to close issues: 27 days
- Average time to close pull requests: N/A
- Total issue authors: 7
- Total pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- teresa-rummel (9)
- Lygeri-Sakellaridi (7)
- ivvukovic (2)
- YecLab (1)
- iamnicogomez (1)
- Gesmira (1)
- daniquebax (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 303 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
cran.r-project.org: grandR
Comprehensive Analysis of Nucleotide Conversion Sequencing Data
- Homepage: https://github.com/erhard-lab/grandR
- Documentation: http://cran.r-project.org/web/packages/grandR/grandR.pdf
- License: Apache License (≥ 2)
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Latest release: 0.2.6
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- MASS * imports
- Matrix * imports
- cowplot * imports
- ggplot2 * imports
- grDevices * imports
- lfc * imports
- methods * imports
- minpack.lm * imports
- numDeriv * imports
- parallel * imports
- patchwork * imports
- plyr * imports
- reshape2 * imports
- stats * imports
- utils * imports
- ComplexHeatmap * suggests
- DESeq2 * suggests
- DT * suggests
- RColorBrewer * suggests
- RCurl * suggests
- Seurat * suggests
- VGAM * suggests
- circlize * suggests
- clusterProfiler * suggests
- cubature * suggests
- eulerr * suggests
- fgsea * suggests
- ggrepel * suggests
- graphics * suggests
- gsl * suggests
- htmltools * suggests
- knitr * suggests
- labeling * suggests
- lamW * suggests
- matrixStats * suggests
- monocle * suggests
- msigdbr * suggests
- quantreg * suggests
- rclipboard * suggests
- rlang * suggests
- rmarkdown * suggests
- scales * suggests
- shiny * suggests