HistoneMod

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HistoneMod is an R package for interactive analysis of histone post-translational modifications (PTMs) from Skyline-like peptide-level CSV exports. It provides a local Shiny application for end users together with a small programmatic API for preprocessing and visualization in scripted workflows.

Starting with version 0.6.2, HistoneMod is distributed as an installable R package rather than as an online hosted Shiny service. The recommended workflow is therefore to install the package once and run the application locally from R.

Features

• Validates MS1 and Sample input tables before analysis.
• Computes relative peptide abundances across replicates and groups.
• Provides interactive PCA, heatmap, and barplot views in a single Shiny workflow.
• Supports plot export, wide-format table export, and quick PDF reporting.
• Exposes reusable preprocessing and plotting helpers for scripted analyses.

Installation

Install HistoneMod from GitHub with dependencies enabled:

install.packages("remotes")
remotes::install_github("jiehua1995/HistoneMod", dependencies = TRUE)

HistoneMod declares its required runtime dependencies in DESCRIPTION, so they are installed automatically as part of package installation.

If you already cloned the repository locally, you can also install from the package directory:

remotes::install_local("HistoneMod", dependencies = TRUE)

Launch the application

For normal use, start the local Shiny application with:

HistoneMod::runHistoneMod()

After the app opens, you can either upload your own MS1 and Sample CSV files or use the built-in demo actions in the sidebar:

• Load Demo Data loads the packaged demo dataset directly into the app.
• Copy Demo Files copies the packaged demo CSV files into a folder that you choose on your local machine.

If you want the Shiny application object itself:

app <- HistoneMod::histonemod_app()
shiny::runApp(app)

Input data

The application expects two comma-separated CSV files. Example layouts are shown below.

MS1 file example

Protein Name	Peptide Note	Replicate Name	Total Area MS1	Isotope Label Type
H3_3-8	H3_3_8_K4_un	SampleA_rep1	4320000000	light
H3_3-8	H3_3_8_K4_me3	SampleA_rep1	1680000000	light

Sample file example

Replicate Name	Group	Replicate No
SampleA_rep1	SampleA	1
SampleA_rep2	SampleA	2

Because HistoneMod uses read.csv(), column names with spaces, such as Protein Name, are automatically converted by R to dotted names such as Protein.Name after import. Skyline exports with space-separated headers are therefore accepted. CSV files produced under different operating systems, language settings, or software versions may vary slightly, but standard comma-separated files are supported as long as the required columns are present.

Bundled demo data

HistoneMod ships with a small packaged demo dataset for local exploration and training. The bundled demo data are derived from the structure of real histone modification result tables, but sample identifiers were anonymized, numeric values were randomized, and the content was simplified to retain only four representative histone modification states.

You can access the packaged demo files from R with:

system.file("extdata", "MS1_demo.csv", package = "HistoneMod")
system.file("extdata", "samples_demo.csv", package = "HistoneMod")

Package tutorial

Open the bundled vignette with:

vignette("tutorial", package = "HistoneMod")

Programmatic API

Most users only need the Shiny interface. For scripted analyses, the following functions are exported:

• depends_check()
• histonemod_app()
• runHistoneMod()
• percentage_calculation()
• plot_pca()
• plot_heatmap()
• plot_barplot_single()

Dependency management

depends_check() can optionally install missing packages with pak, which is useful when you prefer a single dependency manager for packages from both CRAN and Bioconductor:

HistoneMod::depends_check(install_missing = TRUE)

Project information

• Maintainer: Jie Hua
• Contributors: Marco Borso, Beyza Bozdag
• Supervisor: Axel Imhof
• Research group: Imhof Laboratory
• Institution: Ludwig Maximilian University of Munich

Support

Please use the issue tracker for bug reports, feature requests, and installation questions:

• GitHub Issues

Citation

Jie Hua et al. (2026). jiehua1995/HistoneMod: v0.6.2. Zenodo. https://doi.org/10.5281/zenodo.20831990