Welcome to maelstRom’s readme!
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Modeller of allele-specific transcriptomics maelstRom, version 1.1.11
maelstRom is the Modeller of Allele-Specific Transcriptomics, an R package providing extensive functions for various RNAseq-based allelic analyses. This ranges from basic tasks such as (solely) RNAseq-based genotyping, to the analysis of more complex population-level phenomena such as (differential) allelic bias, allellic divergence and (loss of) imprinting analyses. More information about what these are and how to model them using maelstRom can be found in the package vignette.
maelstRom requires a standard computer (server) with sufficient RAM for in-memory operations.
This package is supported for Windows, Linux and MacOS. The package has been tested on the following systems:
maelstRom is an R software package with additional C/C++ code under-the-hood, and as such relies on (versions listed are those used for maelstRom’s latest test, though more recent versions should work fine as well):
Furthermore, maelstRom relies on other R packages for its operations, which are listed in the tutorial: https://biobix.github.io/maelstRom/articles/maelstRom_Allelic_Dispersion_tutorial.html#session-info
If you want to install maelstRom in a conda environment including an R-installation, the following bash commands sets up the previously listed software dependencies, then opens the environment, and launches R:
Setting up this environment takes about 9 minutes on a linux-based server (Ubuntu 18.04; bionic)
maelstRom source code can be found on its associated Github page: https://github.com/Biobix/maelstRom. As such, maelstRom can be installed using the install_github function from R’s devtools package:
library(devtools)
install_github("BioBix/maelstRom")From a clean R installation (e.g. as in the conda environment set up previously), this installation takes about 2 minutes.
For a local installation, rtools will be required. In case the code chunk above throws the error ERROR: loading failed for 'i386', running the following instead potentially solves the issue:
library(devtools)
install_github("BioBix/maelstRom", INSTALL_opts=c("--no-multiarch"))maelstRom contains a vignette going over its entire dAD anaylis pipeline, which can be found here: https://biobix.github.io/maelstRom/articles/maelstRom_Allelic_Dispersion_tutorial.html
Besides this vignette, there’s also a tutorial on further exploration of maelstRom’s dAD results: https://biobix.github.io/maelstRom/articles/maelstRom_results_exploration.html as well as a tutorial on (differential) imprinting analyses using maelstRom: https://biobix.github.io/maelstRom/articles/maelstRom_imprinting_tutorial.html.
Running the entire vignette takes about an hour on a standard computer (local installation; Windows 10) if parallellization is not used (single-core). Enabling parallellization when running maelstRom on large-scale datasets on server is advised.
maelstRom has an associated paper pending publication. Coming soon…
For theoretical/technical questions or issues while using the maelstRom package, please contact me at cedric.stroobandt@ugent.be; for everything else, contact Tim De Meyer at tim.demeyer@ugent.be.