TranscriptomeReconstructoR

TranscriptomeReconstructoR is an R package for data-driven annotation of transcriptomes.

Installation

Install the development version from GitHub using devtools:

if (!"devtools" %in% rownames(installed.packages())) {
    install.packages("devtools")
}
devtools::install_github("Maxim-Ivanov/TranscriptomeReconstructoR", build_vignettes = TRUE, ref = "main")

If the Bioconductor dependencies were not resolved automatically by devtools::install_github(), please install the required Bioconductor packages manually:

BiocManager::install(c("GenomicRanges", "GenomicAlignments", "rtracklayer"))

Linux users may need to resolve some additional dependencies to install devtools. For example, on Ubuntu 20.04:

sudo apt-get install libssl-dev libcurl4-openssl-dev libxml2-dev

Mac users may need Xcode terminal tools to be installed (otherwise the brio dependency may fail to compile). In addition, the collections dependency may not compile properly on MacOS X El Capitan 10.11 and should be installed from the binary package on CRAN:

install.packages("collections", type = "binary")

When TranscriptomeReconstructoR is finally installed, load it:

library(TranscriptomeReconstructoR)

User manual

The vignette contains everything you want to know about TranscriptomeReconstructoR:

• A simple usage scenario (the example dataset is provided);
• Detailed description of the underlying algorithm;
• Considerations regarding the choice and pre-processing of the input datasets.

browseVignettes("TranscriptomeReconstructoR")

or

vignette("TranscriptomeReconstructoR", package = "TranscriptomeReconstructoR")