Installation

Requirements and dependencies

The rnaends package is fully developed in R (>= 4.4.2) and only relies on CRAN or BioConductor packages.

Installation of required packages manually

Install the following packages from CRAN (with their minimum version) with your preferred installation method:

remotes >= 2.5.0
ggupset >= 0.4.0
tidyverse >= 2.0.0
VGAM >= 1.1-9

Typically, this would lead to:

install.packages("remotes")
install.packages(c("ggupset", "tidyverse", "VGAM", "BiocManager"))

Install the following packages from BioConductor:

DSS >= 2.54.0
Rbowtie >= 1.46.0
Rsamtools >= 2.22.0
Rsubread >= 2.20.0
ShortRead >= 1.64.0
survcomp >= 1.56.0

Typically:

BiocManager::install("DSS")
BiocManager::install("Rbowtie")
BiocManager::install("Rsamtools")
BiocManager::install("Rsubread")
BiocManager::install("ShortRead")
BiocManager::install("survcomp")

Then, install rnaends:

remotes::install_gitlab("rnaends/rnaends")

Note: It has been tested on a fresh install of R (4.4.2) and RStudio on Windows 11 without any environment.

See de DESCRIPTION file for version details.

Installation of required packages with an environment manager (conda or mamba)

We recommend the use of mamba (or conda) environment to ensure proper execution of all the features.

Download the environment exported file: https://gitlab.com/rnaends/rnaends/-/raw/main/rnaends.conda.env.txt

Then, use conda or mamba to re-create it:

mamba env create --name rnaends --file rnaends.conda.env.txt

Then, use it (after activation):

mamba activate rnaends
# then use R or Rstudio
rstudio

Then proceed with the following section to install the package from GitLab.

Install from GitLab repository

The installation should work seemlessly by running the following command in R, but depending on your setup, conflicts can occur and it might be necessary to follow the steps of previous sections (manual install or through conda/mamba environment manager).

From the R console, use the install_gitlab function from the remotes package.

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

remotes::install_gitlab("rnaends/rnaends")

Source code

Complete source code is available at https://gitlab.com/rnaends/rnaends.

A local copy can be downloaded with git:

git clone https://gitlab.com/rnaends/rnaends.git