{"title":"ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression.","authors":"Alex C H Liu, Steven M Chan","doi":"10.1093/bioinformatics/btae660","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>We present ADTGP, an R package that uses Gaussian process regression to correct droplet-specific technical noise in single-cell protein sequencing data. ADTGP improves the interpretability of the data by modeling the distribution of protein expression, conditioned on equal isotype control counts across cells. ADTGP is written in R and needs only the protein raw counts, isotype control raw counts, and a design matrix to run.</p><p><strong>Availability and implementation: </strong>ADTGP can be installed from https://github.com/northNomad/ADTGP. It depends on Stan and the R package 'cmdstanr'.</p>","PeriodicalId":93899,"journal":{"name":"Bioinformatics (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568108/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics (Oxford, England)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btae660","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
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Abstract
Summary: We present ADTGP, an R package that uses Gaussian process regression to correct droplet-specific technical noise in single-cell protein sequencing data. ADTGP improves the interpretability of the data by modeling the distribution of protein expression, conditioned on equal isotype control counts across cells. ADTGP is written in R and needs only the protein raw counts, isotype control raw counts, and a design matrix to run.
Availability and implementation: ADTGP can be installed from https://github.com/northNomad/ADTGP. It depends on Stan and the R package 'cmdstanr'.
摘要：我们介绍的 ADTGP 是一个 R 软件包，它使用高斯过程回归校正单细胞蛋白质测序数据中的液滴特异性技术噪声。ADTGP 通过对蛋白质表达的分布进行建模，并以各细胞的同种型对照计数相等为条件，提高了数据的可解释性。ADTGP 用 R 语言编写，运行时只需要蛋白质原始计数、同种型对照原始计数和设计矩阵：ADTGP 可从 https://github.com/northNomad/ADTGP 安装。它依赖于 Stan 和 R 软件包 "cmdstanr"。
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