Version

Pipeline Version

  • PhIP-Seq Analysis Pipeline Version: 0.5.0

  • Adapted from: phip-flow by the Matsen Group

Software Dependencies

Core Pipeline

Tool

Purpose

Nextflow

Workflow orchestration

phippery

PhIP-Seq data structures, normalization, and Z-score modeling

Bowtie2

Short/long read alignment against peptide library

SAMtools

BAM processing, sorting, indexing, and counting

Statistical Analysis (Python)

Library

Purpose

pandas

Data manipulation

numpy

Numerical computation

scipy

Statistical distributions (Z-score to p-value conversion)

statsmodels

Multiple testing correction (Benjamini-Hochberg FDR)

plotly

Interactive heatmap visualizations

Statistical Analysis (R, Optional)

Library

Purpose

PhIPData

Bioconductor PhIP-Seq data class

beer

Bayesian Enrichment Estimation in R

edgeR

Empirical Bayes differential enrichment

Visualization

Library

Purpose

Streamlit

Interactive web dashboard

Mol*

3D protein structure viewer (PDBe Web Component)

Plotly

Interactive heatmaps

Reference Data

IEDB Database

PDB Structures

  • Source: RCSB Protein Data Bank

  • Description: 3D protein structure files (PDB/CIF format) used for mapping enriched epitopes onto protein structures in the Streamlit dashboard.

References

  1. Mohan, D., et al. (2018). PhIP-seq characterization of serum antibodies using oligonucleotide-encoded peptidomes. Nature Protocols.

  2. Larman, H. B., et al. (2011). Autoantigen discovery with a synthetic human peptidome. Nature Biotechnology.

  3. Xu, G. J., et al. (2015). Comprehensive serological profiling of human populations using a synthetic human virome. Science.

  4. Galloway, J. G., et al. (2023) phippery: a software suite for PhIP-Seq data analysis. Bioinformatics.

  5. Di Tommaso, P., et al. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology.