VDJdb in 2019:database extension, new analysis infrastructure and a T-cell receptor motifcompendium. Nucleic Acids Res 48: D1057–D1062 (2020). doi: 10.1093/nar/gkz874 [3] Zhang W, et al. A framework forhighly multiplexed dextramer mapping and prediction of T cell receptorsequences to ...
A complete T-Cell Receptor (TCR) analysis is carried out, harnessing the principles of the 5'RACE technology. This enables the acquisition of full TCR sequences, facilitating comprehensive studies on the impact of Complementarity Determining Regions 1 and 2 (CDR1/2) on Major Histocompatibility Com...
In this chapter, we explain the T-cell receptor (TCR) sequence data analysis pipeline, Tcrip, that was developed for analyzing millions of cDNA sequence reads generated by high-throughput sequencers. Using Tcrip, we can dissect TCR-α and TCR-β sequences into specific segments and estimate ...
VDJdb in 2019:database extension, new analysis infrastructure and a T-cell receptor motifcompendium. Nucleic Acids Res 48: D1057–D1062 (2020). doi: 10.1093/nar/gkz874 [3] Zhang W, et al. A framework forhighly multiplexed dextramer mapping and prediction of T cell receptorsequences to ant...
四、组库的重叠分析(Repertoire overlap analysis) tcR提供了许多基于clonotypes之间共享的cloneset来评估相似度的函数,处理数据框数据。 1. 重叠量化(Overlap quantification) repOverlap 函数是计算cloneset重叠系数的所有函数的通用接口 (1)共享克隆型的数量
Aran A, Lázaro G, Marco V, Molina E, Abancó F, Peg V, Gión M, Garrigós L, Pérez-García J, Cortés J, Martí M. Analysis of tumor infiltrating CD4+ and CD8+ CDR3 sequences reveals shared features putatively associated to the anti-tumor immune response. Front Immunol. 2023 Aug ...
Sequence analysis of t-cell repertoires in health and disease. Genome Med. 5, 98 (2013). Article PubMed PubMed Central Google Scholar Danilova, L. et al. The mutation-associated neoantigen functional expansion of specific T cells (manafest) assay: a sensitive platform for monitoring antitumor...
4) Nucleotide.sequence :CDR3序列片段 5) Nucleotide.sequence.P:有 P-insertions的CDR3序列 注:tcR所有字符串都属于“character”类,而不是“factor”类。因此,应该使用带有参数stringsAsFactors=FALSE的R解析函数。 二、描述性统计量 1. 克隆集汇总Cloneset summary (1)cloneset.stats() cloneset.stats()用于获...
tcrsingle-cellsequence-analysismixed-effects-modelstreg UpdatedJan 28, 2025 Jupyter Notebook yutanagano/sceptr Star10 Simple Contrastive Embedding of the Primary sequence of T cell Receptors bioinformaticstransformerimmunologytcrimmunoinformaticstcr-repertoirecontrastive-learningprotein-language-model ...
SequenceAnalysisoftheTCRBCDR3RegionofTCellClonesinColorectalCancer LIHui—fang,WANYuan—lian,LIUYu—cun,YANGYong-hong,ZHUPing PFirstHosNmlofPekingUniversity.Beijing100034,China Abstract:ObjectiveTostudythemolecularcharacteristicsofanti— tumorTcellclonesbyanalyzingthese— ...