Vogl Lab

Tools & Docs

Software developed in the lab for PhIP-seq data, the peptide libraries behind our screens, and the computing resources we use. Each package has its own documentation site; lab members find the internal documents here after logging in.

Vogl Lab on GitHub

R packages

3 entries

  • phiper

    End-to-end toolkit for PhIP-seq data analysis.

    Docs GitHub

  • phiperio

    PhIP-seq import and export, parsing, validation and standard data objects for the phiper ecosystem.

    Docs GitHub

  • vecmatch

    Generalized propensity scores and matching of multiple groups.

    Docs GitHub CRAN

Pipelines & analysis

4 entries

  • phipflow

    Nextflow pipeline that runs the phiper workflow on LiSC (SLURM, Apptainer) and renders Quarto reports.

    GitHub

  • phipml

    Reproducible PhIP-seq classification: Random Forest and XGBoost, nested cross-validation, SHAP, validation in external cohorts.

    Docs GitHub

  • phipsurv

    Survival analysis with XGBoost-Cox models: nested cross-validation, Bayesian tuning, time-dependent AUC, SHAP.

    GitHub

  • phip_seq_tools

    Earlier lab scripts for PhIP-seq: ZIGP normalization, mapping and counting, R helpers, a Snakemake workflow for LiSC.

    Private repository

Peptide libraries

3 entries

  • ATC2

    The Agilent, Twist and Corona2 libraries: peptide and protein metadata.

    Docs

  • ICAM

    The ICAM library: peptides, source proteins, taxonomy and construction labels.

    Docs

  • Human proteome

    300,000 peptides from the human proteome, with their metadata.

    Docs

Data infrastructure

3 entries

  • noxDB

    The lab's PhIP-seq metadata database: schema, migrations, Python API and maintenance scripts.

    Docs GitHub

  • nox-web

    The code of this website, including the lab's noxDB submission forms.

    Private repository

  • Grafana

    Dashboards over the noxDB PhIP-seq data.

    Grafana Lab login

    Only reachable from the LiSC network: connect from the university network, or have your address allowed through the LiSC firewall.

Computational resources

2 entries

  • LiSC

    Life Science Compute Cluster, University of Vienna: high-performance computing for bioinformatics.

    Website

  • ASC

    Austrian Scientific Computing, formerly the Vienna Scientific Cluster: supercomputers shared by Austrian universities.

    Website

Internal documents

Lab only

Lab members: log in to see the internal documents.

Lab login