Resource.
Tool
PGX Team on GitHub
Explore our open-source tools and projects on GitHub.
Immune recognition
DeepHLApan
A deep learning approach used for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC.
MultiMHC
A dual-pathway deep learning framework for peptide-major histocompatibility complex (pMHC) binding prediction that integrates complementary sequential context and contact-topology representations.
TSNAD
An integrated software for cancer somatic mutation and tumour-specific neoantigen detection from NGS data.
DeepCIP
A deep learning method for the prediction of internal ribosome entry sites (IRES) of circRNAs.
DeepTAP
A deep learning approach used for predicting high-confidence TAP-binding peptide.
COVEP
An ensemble pipeline for coronavirus B/T cell epitopes prediction.
Cancer drivers
CanDriS
A statistical framework for posterior profiling cancer-driving sites based on recurrent somatic mutations.
CN/CS-calculator
A site-specific framework for comprehensively deciphering selective landscape in the cancer genome.
MODIG
A GAT-based model designed for generating gene representation from a multi-dimensional gene network for the identification of cancer driver genes.
Protein evolution
DIVERGE
A python package and web server for large-scale analysis of functional divergence across multi-gene families.
TEMPO
A transformer-based mutation prediction framework for SARS-CoV-2 evolution.
sitePS
A statistical framework for deciphering the phylogenetic age of each amino acid position in the sequence.
TCR_evo
An innovative platform that integrates experimental validation data from mammalian cell surface display and deep sequencing with deep learning frameworks for high-throughput T-cell receptor (TCR) engineering.
Multi-omics analysis
MATTE
A pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis.
Spanve
A statistical method for detecting downstream-friendly spatially variable genes in large-scale spatial transcriptomics data.
TopicVI
A python package that implements topic modeling to define cell subtypes or states based on prior gene programs.
CHORD
A cross-species integration framework for joint representation learning across gene, cell and cell-type levels.
ORIGAMI
A multi-omics, gene-centric deep learning framework that reconstructs functional cis-regulatory networks constrained by transcriptional output.
Database
Immunoinformatics
TSNAdb
Tumor-Specific NeoAntigens database.
TRAIT
T-cell Receptor Antigen InTeraction database.
ImmuCEdb
Immune Cell Engager database.
COVIEdb
Coronaviruses Immune Epitope database.
CovEpiAb
Human Coronaviruses Immune Epitope and Antibody database.
scMOVIR
Single-Cell Multi-Omics database for Viral Infections and Immune Responses.
Cancer multi-omics
OncoTriMD
Cancer-type-centric Multi-scale Oncogenic Driver database.
CandrisDB
Cancer-Driving Site Profiling database.
LymphomaDB
Disease-drug-biomarker knowledge base for Lymphoma.
CFPCA
Chinese Familial Prostate Cancer Multi-omics database.
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