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.
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.
If you use this package, please cite:
Gregoricchio S. et al., Nucleic Acids Research (2022)
doi: 10.1093/nar/gkac613
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"))Certain functions of this package require that deeptools is installed on your system. For more information see the deepTools 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.
Certain functions of this package require that bedtools is installed on your system. For more information see the bedTools 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
- Fedora/Centos:
# 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)With the package a PDF manual and a vignette are available.
The vignette can be inspected on R as well by typing browseVignettes("Rseb").
A list of all releases and respective description of changes applied could be found here.
For any suggestion, bug fixing, commentary please report it in the issues/request tab of this repository.
This package is under a GNU General Public License (version 3).