All scripts used in this study are available on the TMPL wiki as a zip package: http://tmpl.arizona.edu/dokuwiki/doku.php?id=bioinformatics:scripts:vsb and on github: http://github.com/simroux/virsorter-curated-dataset-scripts-package.
To rectify this, we have now prepared the scripts used to produce the results in this manuscript for public release on our lab wiki (the corresponding link: http://tmpl.arizona.edu/dokuwiki/doku.php?id=bioinformatics:scripts:vsb) and a GitHub repository (https://github.com/simroux/virsorter-curated-dataset-scripts-package).
We highly encourage the community to use the 3D printable crystal structure dataset, Jmol scripts, and Jmol 3D Print and Crystal Symmetry Explorer websites to advance their research, education, and outreach efforts with 3D printed molecular models.
The datasets and scripts supporting the conclusions of this article are available in the figshare repository, https://dx.doi.org/10.6084/m9.figshare.org/10.6084/m9.figshare
Datasets and scripts (Perl Language) are available as additional files (see Additional File 2).
As multi-allelic markers would appear to be duplicated in the dataset, the script will preserve incompatible duplicates.
We created additional datasets using scripts; FPKM > 3 using extract_gtf.py, TSS's using get_tss_bed.py and TTS using get_tts.py.py
Although there are ways to manipulate multigenic datasets using scripts, this requires programming skills, and in practice experimental population geneticists often do that manually.
These details were in the prior, PeerJ publication that describes the VirSorter tool, but we now also point readers to these details in the current manuscript (subsection "Dataset and script availability").
For loading data from the provided datasets, a script that can load individual spectra or images is provided.
A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available.
