Here, we propose a reverse epitope discovery technique, which, instead of using large pools of peptides to identify reactive T cells, utilizes TCR repertoire sequencing data as the means to predict immunodominant epitopes. The core idea of the approach is to combine information from large, ...
Learn about our SMARTer approach to single T-cell sequencing that obtains alpha-beta pairing information.
Deep learning algorithms have been utilized to achieve enhanced performance in pattern-recognition tasks. The ability to learn complex patterns in data has tremendous implications in immunogenomics. T-cell receptor (TCR) sequencing assesses the diversity
Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data DeepTCR is a python package that has a collection of unsupervised and supervised deep learning methods to parse TCRSeq data. To see examples of how the algorithms can be used on an example datasets, see the subdirectory...
T-cell receptor repertoire analysis based on RNA sequencing data from tumor cells and tumor-infiltrating lymphocytes. 基于肿瘤细胞和肿瘤浸润性淋巴细胞的RNA测序数据的T细胞受体谱系分析 背景:T细胞受体(TCR)被认为是癌症进展和治疗反应的指标。以前的方法主要集中在外周血或新鲜的肿瘤组织上,有时在临床环境中受到...
[8] Pai J A, Satpathy A T. High-throughput and single-cell T cell receptor sequencing technologies[J]. Nature methods, 2021, 18(8): 881-892. [9] Jiang, X., et al., Comprehensive TCR repertoire analysis of CD4(+) T-cell subsets in rheumatoid arthritis. J Autoimmun, 2020. 109: p...
TCR β amplification and sequencing: IlluminaHiSeq system,high-throughput sequencing TCR repertoire analysis: Shannon Index, Diversity 75 (D75), Singleton Index, Gini-Simpson Index Data analysis: SPSS version 22.0, GraphPad Prism, Dunnett's multiple comparisons test, Kaplan–Meier curves, Mann–Whitne...
Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data deep-learningimmunologyrepertoiretcrtcr-repertoireadaptive-immunity UpdatedFeb 15, 2023 Jupyter Notebook houseofcat/turbocookedrabbit Sponsor Star108 Code Issues Pull requests ...
Cogent NGS Immune Profiler is compatible with rhesus macaque TCR sequencing data Takara Bio’s Cogent NGS Immune Profiler v1 (CogentIP) performs its TCR-seq read alignment using the human genome as a reference. Here, we validate CogentIP as an appropriate choice f...
21 All sequencing was done using the Illumina MiSeq platform, performed at the Norwegian Sequencing Center. All TCR sequence data were deposited in the European Genome-Phenome Archive (accession number EGAS00001003897). TCR repertoire analysis Obtained reads from the Illumina sequencing was processed ...