eIF5A_hypusination_inhibition_silac

A dynamic SILAC experiment to explore the impact of eIF5A hypusination inhibition by GC7 on nascent protein

Analysis of an experiment to study eIF5A-dependent translation using GC7 inhibition of eIF5A hypusination and dynamic SILAC to measure nascent proteomics.

Directory structure:

• raw: PSM and peptide-level output from PD. One for each experiment
• notebooks: R markdown notebooks for all analysis. Run in denoted order.
• results: Output from analysis notebooks
• external: Data from previous studies
• figures: Plots for publication

Dependencies for R markdown notebooks:

All R packages.
For CRAN use install.packages()
For Bioconductor, use BiocManager::install()
Both the above functions will take multiple package names, e.g BiocManager::install(c(GO.db, MSnbase))

CRAN
dplyr
here
ggbeeswarm
ggplot2
glmnet
ggrepel
gplots
gtools
parallel
pbapply
here
pRoc
parallel
pbapply
RColorBrewer
stringr
tidyr
writexl

Bioconductor
MSnbase
GO.db
biobroom
goseq
limma
DEqMS
Biostrings

R-universe Install uniprotREST with:
install.packages("uniprotREST", repos = "https://csdaw.r-universe.dev")

Github
Install camprotR with:
remotes::install_github("CambridgeCentreForProteomics/camprotR", build_vignettes = TRUE)