Personalized Immunotherapy Research Lab

Open Source Computational Tools

PIRL uses and creates a variety of computational tools for our work in genomics and computational immunology. Many of these tools are carried over from previous work by the Vincent Lab at UNC, and OpenVax. Newer tools which are developed by PIRL will be listed below.

TCR-TRANSLATE

TCR-TRANSLATE

A sequence-to-sequence language model for antigen-specific TCR design that addresses data sparsity through techniques from low-resource machine translation.

LENS

LENS

Tumor antigen prediction pipeline used to curate tumor-specific predicted MHC ligands from a variety of mutational and expression sources.

ACE

ACE

Multiplex ELISpot assay design and deconvolution tool for determining epitope-specific T-cell responses from a large number of candidate peptides.

MHCgnomes

MHCgnomes

A tricky part of constructing large immunological datasets is dealing with the chaotic variability in naming of MHC molecules across species and within different research communities. MHCgnomes is a parser for MHC nomenclature which uses several reference data sources and a robust parsing strategy to standardize MHC nomenclature from a variety of different naming schemes you might encounter in the wild.

RAFT

Reproducible Analyses Framework and Tools: infrastructure for configuring and running reproducible Nextflow analyses.

Exacto

A long-read toolkit for mutant proteoform prediction that integrates DNA and RNA variants, assembles transcripts, and translates them into annotated proteoforms and mutant peptides.

All public repositories

Pulled from github.com/pirl-unc when the site is built.

RepositoryDescriptionLanguageLast push
weirdo Metrics of immunological foreignness for candidate T-cell epitopes Jupyter Notebook
pirlygenes Gene sets used for cancer immunotherapy expression analysis Python
presto All of T-cell:pMHC prediction in one model Python
hitlist Curated mass spectrometry evidence for MHC ligand data from IEDB and CEDAR Python
oncoref Curated cancer reference data: ontology, TMB, incidence/mortality, and expression. Bottom-of-stack for the openvax/PIRL libraries. Python
pirl-unc.github.io pirl.unc.edu Python
mhcgnomes Parsing MHC nomenclature in the wild Python
mhcseqs MHC sequences Python
io-resistance-genie [WIP / experiment] Living literature review of resistance to immune checkpoint inhibitors Python
DoesExactoWorkYet Simple end-to-end test of Exacto Python
vmwhere exploring microsatellites in the human genome Python
tsarina Tumor Specific Antigen discovery: personalized cancer immunotherapy targets from curated shared antigen data Python
trufflepig Step-by-step RNA tumor analysis driven by pirlygenes gene sets — subsumes pirlygenes.analyze as many composable sub-commands with serializable intermediate state. Python
tcrsift Python
exacto Long-read toolkit for mutant proteoform prediction - somatic/germline DNA and RNA assembly, variant calling, integration, and translation Rust
singlecell_images Docker files for images containing seurat + scCDC and seurat + decontx ( celda ) Shell
alcohol-immunotherapy Data and code for "Alcohol use reduces the efficacy of anti-PD1 immunotherapy by disrupting anti-tumor immunity"
runplz Tiny Modal-shaped job harness Python
raft-ui RAFT web interface for generating manifests and configuration files. HTML
nexus A command-line streamliner for Nextflow bioinformatics pipelines. Nextflow
aggrescan3d-slurm-workflow Python
pdockq-slurm-workflow Python
vstol Variant Standardization, Tabulation, and Operations Library Python
io-shieldbreak Python
squid-tui Squid-TUI (Slurm QUeue Interactive Dashboard): Terminal UI (TUI) for organizing, filtering, and managing SLURM jobs. Python
golfy Heuristic solver for pooled peptide experiment design Jupyter Notebook
perseo Personalized cancer immunotherapy target selection from curated shared antigen data Python
hf-tcr HuggingFace Scaffolding for EZ TCR Generation and Evaluation Python
TCRpMHCdataset Python Class for Handling Many-to-Many Nature of TCR::pMHC Data Python
pirl-blog-notebooks Jupyter notebooks accompanying PIRL Blog posts Jupyter Notebook
PRAME_in_NUT_Carcinoma R
tahp Tumor Antigen Heterogeneity Profiler Python
pdf-reports Helping code for compiling plots and other outputs into presentation pdfs. R
ace Deep learning-powered multiplexed ELISpot assay design and deconvolution of pool readouts for immunogenic peptide identification. Jupyter Notebook
datasetprep Methods to make life easier when preparing datasets for analysis. R
lens_demo_workflow_outputs HTML
binfotron R
housekeeping R
rserver-binfotron Dockerfile
translate-pacbio-reads-for-bbn963 Jupyter Notebook
longread-fusion-transcript-pipeline R
lineardesign docker image to run externally developed LinearDesign software
MiXCR Dockerfile and script to run MiXCR Dockerfile
pvacitopes Epitope selection from pVACtools output Python
bbn963_fusion_transcript_pipeline A pipeline associated with the longread fusion pipeline used to extract fusions from our associated pacbio bbn963 data. R
NeoantigenProfiler R
nutm1-fusions Hunting for T-cell epitopes in recurrent NUTM1 somatic fusions Jupyter Notebook
lens Landscape of Effective Neoantigens Software
yolotrim Heuristic read trimming for PacBio IsoSeq data Rust
PostRNASeqAlign R
nara NUTM1 Associated Recurrent Antigens: possible T-cell targets on NUTM1 rearranged neoplasms Jupyter Notebook
rserver-immunesubtypes hosts dockerfile for running immune subtypes package Dockerfile
variform Variant isoform detection for large mutations in long-read RNA sequencing Python
python-project-template Template of a basic Python project Python
coding-guidelines Coding guidelines and recommendations for tools developed by PIRL
rserver rserver Shell
PrePostMiXCR Functions for writing commands and post processing the MiXCR pipeline. R
rserver-postproc-rnaseq Dockerfile to make RStudio server for doing post processing of rnaseq data using the StarSalmon R-package Dockerfile
Landscape-and-Selection-of-Vaccine-Epitopes-in-SARS-CoV-2 Code and data for "Landscape and Selection of Vaccine Epitopes in SARS-CoV-2" Jupyter Notebook
mHA-dockerfile Dockerfile
lenstools Dockerfile
command-line-tools Tools helpful for working with data, nextflow, etc. R
picard Adds magrittr to docker://broadinstitute/picard:2.27.5 to bypass error when using apptainer. Dockerfile
are-we-good CI status of every project we develop and/or help maintain
HLAProfiler R
StarSalmon R
rserver-sc RServer for single cell analyses. Contains monocle3, zinbwave and scRNAseq Dockerfile
VincentLabFormatter R
stig Synthetic T-cell Informatics Generator Python
fastmultiqc Has environment and script for running fastqc and then multiqc on the results. Shell
trust_published Dockerfile for running the original published version of TRUST. Dockerfile
trust Dockerfile for running TRUST 3.0 R
MiXCR-2.1.7 Dockerfile and script to run MiXCR 2.1.7 RNAseq Java
MiXCR-amplicon-2.1.7 Dockerfile & script used for the diversity paper MiXCR amplicon runs. Java
Bowtie2 Dockerfile and examples for using Bowtie2 Shell
tide Dockerfile
rserver-impro Dockerfile
making-sense-of-tesla Jupyter Notebook
.github Personalized Immunotherapy Research Lab at UNC
neoag Mirror of vincentlaboratories / neoag R
fusion-transcript-workflow
ace-analysis HTML
raft Python
bbn963-mutations Exploring long read WGS somatic variants for BBN963 cell line Jupyter Notebook
python-rust-template The purpose of this repository is to test continuous integration using GitHub Actions Python
defense-against-the-dark-arts Course website and resources for BCB 731 HTML
lbg-guide Basic usage tips for the LBG cluster at UNC-CH
Rmbleven An R utility for string comparisons using the mbleven algorithm written in Rcpp. C++
tricking_nextflow_cache This is a minimal code example demonstrating use of the clean_work_files.sh script to delete intermediate files in Nextflow workflows. Nextflow
blogs Repositories for Code Associated with Blog Posts on PIRL Website Jupyter Notebook
immproper T-cell epitope predictor Python
u87-ttf-mutational-signature Mutational signature analysis of U87 glioma cells exposed to Tumor Treating Fields Shell
sv-web-parser-and-visualizer Python
u87-u937-isoseq-demux Demultiplexing of Iso-Seq cell line data Python
metaseq Metadata format for collections of FASTA files containing genomic sequencing reads
SeqPipe Reusable pipeline for sequence alignment and variant calling.
unc-sars-cov-2-sequencing Analysis of SARS-CoV-2 viral sequencing data Jupyter Notebook
isovar-on-mouse-cell-lines-shell-scripts Shell script that runs the RNA aligner star Jupyter Notebook
til-unc.github.io Website for Translational Immunogenomics Lab HTML
klamp SARS-CoV-2 detection from LamPORE sequencing data Python
cd8-tcell-epitope-prediction-data Data for building predictive models of CD8+ T-cell epitopes Jupyter Notebook