ScaffoldMS R package
Enhanced analysis of protein mass spectrometry results provided by Scaffold Proteome software ©.
Installation
remotes::install_gitlab(
"aurelien.brionne/ScaffoldMS",
host = "forgemia.inra.fr",
build_opts = c("--no-resave-data", "--no-manual")
)Quick overview
- Annotate proteins:
ScaffoldMS::post_treatment.
- Identification of the species of origin from Genbank data (taxon, scientific name, common name).
- Gene annotation summary.
- construction of the peptide signature ("pattern") allowing the identification of proteins and their grouping using Blast + suite and clustal omega.
-
perform Linear model statistics from Scaffold Proteome software © quantification files (current view):
ScaffoldMS::quantify. -
Merge pattern alignments (clustalo and blast) results:
ScaffoldMS::merge_alignments. -
Display proteins species count overview:
ScaffoldMS::species_count.
- Proteins abundance profiling:
ScaffoldMS::HCL.
- Proteins abundance plot:
ScaffoldMS::abundance_plot.
