View on GitHub

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.

Download this project as a .zip file Download this project as a tar.gz file

release license forks

Introduction

The concept behind the Rseb (R-package for Simplified End-to-end data Build-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: https://doi.org/10.1093/nar/gkac613


Dependencies/Requirements

Bioconductor libraries

Some functions of this package require Bioconductor libraries. These functions should install automatically with the package. However, if you prefer to manually install Bioconductor and required packages proceed with the Bioconductor installation:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

The required Biocondutor packages are: Biostrings, biomaRt, diffloop, GO.db, rtracklayer, GenomicRanges, AnnotationFilter, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79. To install it manually proceed with:

BiocManager::install(c("Biostrings", "biomaRt", "diffloop", "GO.db", "rtracklayer", "GenomicRanges", "AnnotationFilter", "EnsDb.Hsapiens.v75", "EnsDb.Hsapiens.v86", "EnsDb.Mmusculus.v79"))


deepTools

Certain functions of this package require that deeptools is installed on your system. For more information see the deepTools installation page.


bedTools

Certain functions of this package require that bedtools is installed on your system. For more information see the bedTools installation page.


Installation

# Install devtools from CRAN
install.packages("devtools")

# Or the development version from GitHub:
## install.packages("devtools")
## devtools::install_github("r-lib/devtools")

# Install the Rseb package
devtools::install_github("sebastian-gregoricchio/Rseb",
			 build_manual = TRUE,
                         build_vignettes = TRUE)


Documentation

With the package a PDF manual and a vignette 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.



Contact

For any suggestion, bug fixing, commentary please contact Sebastian Gregoricchio at sebastian.gregoricchio@gmail.com.

License

This package is under a GNU General Public License (version 3).


Contributors

contributors