A collection of Python&R scripts from my PhD research (mostly plant phylogenetics)
This is a partial collection of R and Python (2.XX) scripts I made during my PhD, usable with publicly available datasets and software for (plant) genomics & phylogenetics. Some of the original datasets consisted of huge genomic files and annotations, so instead of including them directly in the repository, I opted for a reference list with download links whenever possible.
Had I known about version control earlier I would have structured things differently, likely into separate repositories for each project, and spent more time in creating mock datasets for testing (this is something I started doing more recently, see for instance test data in 01_FASTA_operations/test_files_for_fasta_EXTRACT-EXTEND).
..Better late than never I guess ;)
Folders 01-03 and Utilities contain scripts I used for general cross-project operations, such as handling of FASTA files and gene functional annotation.
Folders 04-05 are specific to two publications, respectively
Bai, Peviani, van der Horst, et al. (2017). Extensive translational regulation during seed germination revealed by polysomal profiling. The New Phytologist, 214(1), 233–244.
and
Peviani, Lastdrager, Hanson, & Snel (2016). The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. Scientific Reports, 6, 30444.
Folder 05 in particular is an actual pipeline (with steps described in the HOWTO file) I used to resolve a complex gene family phylogeny, combining several different tools and manual inspection of the resulting alignments iteratively (reason why it would be extremely difficult to fully automate).