https://github.com/sebastian-gregoricchio/rseb
An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.
https://github.com/sebastian-gregoricchio/rseb
atac-seq bedtools chip-seq cutandtag daily-tasks data-visualisation data-visualization datamining deeptools genomics ngs qpcr qpcr-analysis r rna-seq statistics
Last synced: 16 days ago
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An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.
- Host: GitHub
- URL: https://github.com/sebastian-gregoricchio/rseb
- Owner: sebastian-gregoricchio
- License: gpl-3.0
- Created: 2020-12-14T15:56:44.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2026-01-26T12:39:20.000Z (5 months ago)
- Last Synced: 2026-04-19T02:40:06.562Z (about 2 months ago)
- Topics: atac-seq, bedtools, chip-seq, cutandtag, daily-tasks, data-visualisation, data-visualization, datamining, deeptools, genomics, ngs, qpcr, qpcr-analysis, r, rna-seq, statistics
- Language: R
- Homepage: https://sebastian-gregoricchio.github.io/Rseb/
- Size: 10.5 MB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
- Citation: citation.cff
Awesome Lists containing this project
README
[](https://sebastian-gregoricchio.github.io/Rseb/LICENSE.md/LICENSE)
[](https://zenodo.org/doi/10.5281/zenodo.13645872)
[](https://github.com/sebastian-gregoricchio/Rseb/fork)
# Rseb [
](https://sebastian-gregoricchio.github.io/Rseb)
An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data managing.
## Introduction
The concept behind the `Rseb` (*R*-package for *S*implified *E*nd-to-end data *B*uild-up) is to provide a toolkit that allows the automation of different type of tasks avoiding retyping of code and loss of time. Furthermore, the advantage is that, in most of the cases, the functions are built in R-language making it suitable for all the operating systems
From a more biological point of view, this package simplifies many downstream analyses of high-throughput data that otherwise would require many hours of code typing and case-to-case adaptation. Moreover, most of the functions aimed to visualize these kind of data are thought to provide a high level of possible customization with a large number of graphical parameters compared to the commonly used already available tools. Another advantage of this package is that it offers multiple methods, with a corresponding visualization, to quantify the difference of signal between samples, in a qualitatively and/or quantitatively way, without any additional coding.
The guide is divided in three parts: the first one will explore some analyses and visualization of RNA-seq data, the second one the representation and quantification of targeted sequencing data (ChIP-seq, ATAC-seq, etc.), while the last part is focused on some of the "general" tools available.
### Citation
If you use this package, please cite:
"HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia."
Gregoricchio S. *et al.*, *Nucleic Acids Research* (2022)
*doi*: [10.1093/nar/gkac613](https://doi.org/10.1093/nar/gkac613)
## Dependencies/Requirements
### Unavailble libraries
Some functions require packages that are noy available anymore on Bioconductor (namely `SUSHI` and `diffloop`).
These can be installed (in the following order) as indicated below:
```r
# Install remotes from CRAN
if (!require("remotes")) install.packages("remotes")
# Install SUSHI package
remotes::install_github("https://github.com/PhanstielLab/Sushi",
build_manual = FALSE,
build_vignettes = FALSE)
# Install diffloop package
remotes::install_github("https://github.com/aryeelab/diffloop",
build_manual = FALSE,
build_vignettes = FALSE)
```
### deepTools
Certain functions of this package require that `deeptools` is installed on your system. For more information see the [deepTools](https://deeptools.readthedocs.io/en/develop/content/installation.html) installation page.
* **Installation via `conda`**: `conda install -c bioconda deeptools`
* **Command line installation using `pip`**: `pip install deeptools`, All python requirements should be automatically installed.
### bedTools
Certain functions of this package require that `bedtools` is installed on your system. For more information see the [bedTools](https://bedtools.readthedocs.io/en/latest/content/installation.html) installation page.
* **Installation via `conda`**: `conda install -c bioconda bedtools`
* **Command line installation**:
- Fedora/Centos: `yum install BEDTools`
- Debian/Ubuntu: `apt-get install bedtools`
- Homebrew (MacOS): `brew tap homebrew/science; brew install bedtools`
- MacPorts: `port install bedtools`
## Installation of `Rseb`
```r
# Install remotes from CRAN
if (!require("remotes")) install.packages("remotes")
# Install the Rseb package
remotes::install_github("sebastian-gregoricchio/Rseb",
build_manual = TRUE,
build_vignettes = TRUE)
```
## Documentation
With the package a [PDF manual](https://sebastian-gregoricchio.github.io/Rseb/Rseb_manual.pdf) and a [vignette](https://sebastian-gregoricchio.github.io/Rseb/doc/Rseb.overview.vignette.html) are available.
The vignette can be inspected on R as well by typing `browseVignettes("Rseb")`.
## Package history and releases
A list of all releases and respective description of changes applied could be found [here](https://sebastian-gregoricchio.github.io/Rseb/NEWS).
-----------------
## Contact
For any suggestion, bug fixing, commentary please report it in the [issues](https://github.com/sebastian-gregoricchio/Rseb/issues)/[request](https://github.com/sebastian-gregoricchio/Rseb/pulls) tab of this repository.
## License
This package is under a [GNU General Public License (version 3)](https://sebastian-gregoricchio.github.io/Rseb/LICENSE.md/LICENSE).
#### Contributors
[](https://sebastian-gregoricchio.github.io/)