Table 4.
Summary of computational tools and resources for immune infiltration and tumor antigen-HLA typing.
| Name | Description | Link |
|---|---|---|
| CIBERSORTx | Provide an estimation of the abundances of member cell types in a mixed cell population | https://cibersortx.stanford.edu/ |
| ImmuCellAI | A unique method for comprehensive T-cell subsets abundance prediction and ICB response prediction | https://guolab.wchscu.cn/ImmuCellAI |
| ImmuCellAI-mouse | A tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction | https://guolab.wchscu.cn/ImmuCellAI-mouse |
| TIMER2.0 | A comprehensive resource for systematical analysis of immune infiltrates across diverse cancer types | http://timer.cistrome.org/ |
| xCell | Digitally portraying the tissue cellular heterogeneity landscape | http://xCell.ucsf.edu/ |
| TIP | A web server for resolving tumor immunophenotype profiling | http://biocc.hrbmu.edu.cn/TIP/ |
| EPIC | Estimating the proportions of immune and cancer cells | http://epic.gfellerlab.org |
| ESTIMATE | Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data | https://bioinformatics.mdanderson.org/estimate/ |
| MCP-counter | Microenvironment cell populations-counter | https://github.com/ebecht/MCPcounter |
| quanTIseq | Constrained least square regression | http://icbii-med.ac.at/software/quantisea/doc/index.html |
| pVAC-seq | Personalized variant antigens by cancer sequencing | https://github.com/griffithlab/pVAC-Seq |
| INTERGTATE-Neo | A pipeline for personalized gene fusion neoantigen discovery | https://github.com/ChrisMaherLab/INTEGRATE-Neo |
| TSNAD | Tumor-specific neoantigen detection | http://biopharm.zju.edu.cn/tsnad/ |
| CloudNeo | A cloud pipeline for identifying patient-specific tumor neoantigens | https://github.com/TheJacksonLaboratory/CloudNeo |
| ScanNeo | Identifying indel-derived neoantigens using RNA-Seq data | https://github.com/ylab-hi/ScanNeo |
| ASNEO | Identification of personalized alternative splicing based neoantigens with RNA-seq | https://github.com/bm2-lab/ASNEO |
| NetMHCpan | Prediction of peptide-MHC class I binding using artificial neural networks | http://www.cbs.dtu.dk/services/NetMHCpan-4.1/ |
| DeepHLApan | Neoantigen prediction considering both HLA-peptide binding and immunogenicity | https://github.com/jiujiezz/deephlapan |
HLA: Human Leukocyte Antigen; ICB: Immune checkpoint blockade; MHC: Major histocompatibility complex.