An extension of LOPIT to explore the subcellular distribution of succinylated peptides
Repository structure:
- raw: PSM-level output from Proteome Discoverer
- shared files: Reference and cRAP fasta files, protein abundances and GO annotations
- notebooks: Analyses in R markdown notebooks, with order indicated by prefix
- results: Intermediate and final outputs from notebooks and plots
- figures: Figure panels for manuscript
- R >= 4.0.3
- tidyverse (CRAN)
- ggrepel (CRAN)
- RColorBrewer (CRAN)
- MSnbase (Bioconductor)
- biomaRt (Bioconductor)
- goseq (Bioconductor)
- pRoloc (Bioconductor)
- camprotR (https://github.com/CambridgeCentreForProteomics/camprotR)
- OptProc (https://github.com/TomSmithCGAT/OptProc)
- pRolocExt (https://github.com/TomSmithCGAT/pRolocExt)