Package 'EpitoScope'

Title: Interactive QC, Visualization, and Immunogenicity Assessment of Immunopeptidomics Data
Description: An interactive R/Shiny application that unifies quality control, visualization, comparative statistics, and MHC class I/II binding prediction for mass-spectrometry-based immunopeptidomics data. It ingests search-engine outputs from PEAKS, FragPipe, DIA-NN, and Spectronaut through a configurable column-mapping layer, and provides publication-ready figure export and relational storage of processed results and binding predictions.
Authors: Yannic Chen [aut, cre]
Maintainer: Yannic Chen <[email protected]>
License: GPL-3
Version: 1.0.0
Built: 2026-09-25 22:39:27 UTC
Source: https://github.com/yannic-chen/EpitoScope

Help Index

This function is to generate the table for column mapping. i.e. which columns are used for what info

Description

This function is to generate the table for column mapping. i.e. which columns are used for what info

Usage

Colum_mapping_table(df, max_chars = 20)

Arguments

df

data.frame to display
max_chars

integer, maximum number of characters to show before truncating. Avoid wide columns

Value

data.frame with HTML for truncated display

Launch the EpitoScope Shiny application

Description

Launch the EpitoScope Shiny application

Usage

run_app(
  input_variable = NULL,
  generate_pseudo_sequence = FALSE,
  custom_schema = NULL,
  custom_signature = NULL,
  replace_schema = FALSE,
  db_path = NULL,
  ...
)

Arguments

input_variable

Optional pre-loaded annotation table. Default NULL.
generate_pseudo_sequence

Logical, passed to the server. Default FALSE.
custom_schema, custom_signature

Optional named lists to extend/replace the schema.
replace_schema

Logical; replace vs. extend the built-in schema.
db_path

SQLite results DB path. Defaults under tools::R_user_dir().
...

Passed to shiny::shinyApp().

Value

A Shiny app object