clustifyr: an R package for automated single-cell RNA sequencing cluster classification.
clustifyr: an R package for automated single-cell RNA sequencing cluster classification.
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DOI：
10.12688/f1000research.22969.1
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发表时间：
2020-01-01
期刊：
影响因子：
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通讯作者：
Riemondy, Kent A
中科院分区：
文献类型：
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作者：
Fu, Rui;Gillen, Austin E;Riemondy, Kent A
从单细胞RNA测序（scRNA-seq）数据中分配细胞类型仍然是一个耗时且容易出错的过程。当前用于标识赋值的包使用有限类型的引用数据，并且通常具有严格的数据结构要求。我们开发了clustifyr R包来利用几种外部数据类型，包括基因表达谱，使用来自scRNA-seq、bulk RNA-seq、微阵列表达数据或签名基因列表的数据来分配可能的细胞类型。我们对基于相关性的方法的各种参数进行基准测试，并实现基因列表富集方法。clustifyr是一款轻量级且有效的细胞类型分配工具，用于兼容各种scRNA-seq分析工作流程。clusteryr可以在https://github.com/rnabioco/clustifyr上公开获取。
Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited types of reference data and often have rigid data structure requirements. We developed the clustifyr R package to leverage several external data types, including gene expression profiles to assign likely cell types using data from scRNA-seq, bulk RNA-seq, microarray expression data, or signature gene lists. We benchmark various parameters of a correlation-based approach and implement gene list enrichment methods. clustifyr is a lightweight and effective cell-type assignment tool developed for compatibility with various scRNA-seq analysis workflows. clustifyr is publicly available at https://github.com/rnabioco/clustifyr.