Package index

FASTA & Protein Processing

Parse FASTA files, digest proteins, and map peptides.

parse_uniprot_fasta()

Read UniProt protein sequences from FASTA.

rank_uniprot_entries()

Assign rank to UniProt entries

proteins_digest()

In silico protein digestion

map_peptides_to_proteins()

Map peptide sequence IDs to proteins using a FASTA file

Protein Group Assembly

Infer protein groups from peptide-to-protein mappings.

assemble_protein_groups()

Assemble protein groups from peptide-to-protein mapping

append_protein_groups_info()

Append extra information to a protein groups frame

default_protein_grouping()

Functions for protein group inference, inspired by the concepts from "MaxQuant's post-computational razor: a massively parallel graphical model for post-processing proteomics data" by K. S. Rudolph et al.

pregrouped_protein_grouping()

Rule for merging proteins that allows for pre-grouping

Visualization

Seer-branded ggplot2 themes and color scales.

theme_seer()

Seer ggplot2 Theme

seer_palette

Seer Color Palette

scale_colour_seer() scale_color_seer()

Seer Color Scale for ggplot2

scale_fill_seer()

Seer Fill Scale for ggplot2

Data Display

Helpers for readable data frame output.

printable()

Prepares a data frame for printing by selecting columns and applying specific transformations.

Code Style

Seer coding style guide for styler.

seer_style()

Seer Styler Guide

Reference Data

Built-in datasets.

plasma_markers_geyer

Plasma Proteins Biomarkers