PASToolsR

PASToolsR is a companion R package that provides utility functions for PAS Notebooks — a collection of data analysis notebooks for the Proteograph Analysis Suite (PAS) platform by Seer.

Features

Proteomics Data Processing

• FASTA Parsing — Read and parse UniProt FASTA files with parse_uniprot_fasta(), extracting protein accessions, gene names, organism, and other metadata.
• In Silico Digestion — Generate theoretical peptides from protein sequences with proteins_digest(), supporting configurable enzyme rules, missed cleavages, and peptide length filters.
• Peptide to Protein Mapping and Protein Group Assembly — Map observed peptides to proteins (map_peptides_to_proteins()) and infer protein groups from peptides (assemble_protein_groups())

Tables and Plots Display

• Seer and PAS ggplot2 Theme for uniform styling of PAS data (see theme_seer() and seer_palette).
• printable() for condensing long protein names etc for readability

Biomarkers Lists

• Curated set of plasma protein biomarkers from Geyer et al. (2019) for assessing sample composition.

Code Style

• seer_style() — A styler style guide matching the PAS Notebook coding conventions

Installation

PASToolsR is not available in CRAN. To install it, the most convenient option is to use pak R package manager:

pak::pkg_install("github::seerbio/PASToolsR")