pepdiff/README.Rmd at master · TeamMacLean/pepdiff · GitHub

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---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# pepdiff <a href="https://teammaclean.github.io/pepdiff/"><img src="man/figures/logo.png" align="right" height="138" alt="pepdiff website" /></a>

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**Differential abundance analysis for proteomics data.**

pepdiff helps proteomics researchers answer: "What's differentially abundant?"

## Features

- **GLM analysis** -- Gamma GLM with emmeans for factorial designs
- **ART analysis** -- Non-parametric alternative for heavy-tailed data
- **Pairwise tests** -- Wilcoxon, bootstrap-t, Bayes factor, rank products
- **Stratified comparisons** -- Analyse effects within factor levels
- **Fit diagnostics** -- Visual checks for GLM model assumptions
- **Rich visualizations** -- Volcano plots, heatmaps, PCA, p-value histograms

## Installation

Install from GitHub:

```r
# install.packages("pak")
pak::pak("TeamMacLean/pepdiff")
```

## Quick Start

```{r example, eval=FALSE}
library(pepdiff)

# Import data
dat <- read_pepdiff(
  "data.csv",
  id = "peptide",
  gene = "gene_id",
  value = "abundance",
  factors = c("treatment", "timepoint"),
  replicate = "bio_rep"
)

# Run differential analysis
results <- compare(
  dat,
  compare = "treatment",
  ref = "ctrl",
  method = "glm"
)

# Visualize results
plot(results)
```

## Documentation

- **[Getting Started](https://teammaclean.github.io/pepdiff/articles/basic_workflow.html)** -- Basic workflow
- **[GLM Analysis](https://teammaclean.github.io/pepdiff/articles/glm_analysis.html)** -- Factorial designs with GLM
- **[ART Analysis](https://teammaclean.github.io/pepdiff/articles/art_analysis.html)** -- Non-parametric alternative
- **[Checking Model Fit](https://teammaclean.github.io/pepdiff/articles/checking_fit.html)** -- Diagnostic plots
- **[Pairwise Tests](https://teammaclean.github.io/pepdiff/articles/pairwise_tests.html)** -- Direct two-group comparisons
- **[Function Reference](https://teammaclean.github.io/pepdiff/reference/index.html)** -- Full API

## Companion Package

**peppwR** answers "How many samples do I need?" (power analysis)
**pepdiff** answers "What's differentially abundant?" (analysis)

See [peppwR](https://github.com/TeamMacLean/peppwR) for experimental design planning.

## Workflow

```mermaid
flowchart LR
    A[CSV] --> B[read_pepdiff]
    B --> C[pepdiff_data]
    C --> D[compare]
    D --> E[pepdiff_results]
    E --> F[plot]

    style A fill:#FFFFCC,stroke:#BD0026
    style B fill:#FD8D3C,stroke:#BD0026,color:#fff
    style C fill:#FFFFCC,stroke:#BD0026
    style D fill:#FD8D3C,stroke:#BD0026,color:#fff
    style E fill:#FFFFCC,stroke:#BD0026
    style F fill:#FD8D3C,stroke:#BD0026,color:#fff
```

## Citation

If you use pepdiff in your research, please cite:

```
MacLean, D. (2026). pepdiff: Differential Abundance Analysis for
Proteomics Data. R package version 1.0.0.
https://github.com/TeamMacLean/pepdiff
```

## Contributing

Contributions welcome! Please open an [issue](https://github.com/TeamMacLean/pepdiff/issues) or submit a pull request.

## License

MIT