Ming Tang1,2,3, Yasin Kaymaz1, Brandon L Logeman2,3, Stephen Eichhorn4, Zhengzheng S Liang2,3, Catherine Dulac2,3, Timothy B Sackton1. 1. FAS Informatics Group, Harvard University, Cambridge, MA, USA. 2. Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA. 3. Howard Hughes Medical Institute, Cambridge, MA, USA. 4. Department of Chemistry, Harvard University, Cambridge, MA, USA.
Abstract
MOTIVATION: One major goal of single-cell RNA sequencing (scRNAseq) experiments is to identify novel cell types. With increasingly large scRNAseq datasets, unsupervised clustering methods can now produce detailed catalogues of transcriptionally distinct groups of cells in a sample. However, the interpretation of these clusters is challenging for both technical and biological reasons. Popular clustering algorithms are sensitive to parameter choices, and can produce different clustering solutions with even small changes in the number of principal components used, the k nearest neighbor and the resolution parameters, among others. RESULTS: Here, we present a set of tools to evaluate cluster stability by subsampling, which can guide parameter choice and aid in biological interpretation. The R package scclusteval and the accompanying Snakemake workflow implement all steps of the pipeline: subsampling the cells, repeating the clustering with Seurat and estimation of cluster stability using the Jaccard similarity index and providing rich visualizations. AVAILABILITYAND IMPLEMENTATION: R package scclusteval: https://github.com/crazyhottommy/scclusteval Snakemake workflow: https://github.com/crazyhottommy/pyflow_seuratv3_parameter Tutorial: https://crazyhottommy.github.io/EvaluateSingleCellClustering/.
MOTIVATION: One major goal of single-cell RNA sequencing (scRNAseq) experiments is to identify novel cell types. With increasingly large scRNAseq datasets, unsupervised clustering methods can now produce detailed catalogues of transcriptionally distinct groups of cells in a sample. However, the interpretation of these clusters is challenging for both technical and biological reasons. Popular clustering algorithms are sensitive to parameter choices, and can produce different clustering solutions with even small changes in the number of principal components used, the k nearest neighbor and the resolution parameters, among others. RESULTS: Here, we present a set of tools to evaluate cluster stability by subsampling, which can guide parameter choice and aid in biological interpretation. The R package scclusteval and the accompanying Snakemake workflow implement all steps of the pipeline: subsampling the cells, repeating the clustering with Seurat and estimation of cluster stability using the Jaccard similarity index and providing rich visualizations. AVAILABILITYAND IMPLEMENTATION: R package scclusteval: https://github.com/crazyhottommy/scclusteval Snakemake workflow: https://github.com/crazyhottommy/pyflow_seuratv3_parameter Tutorial: https://crazyhottommy.github.io/EvaluateSingleCellClustering/.
Authors: Joseph R Knoedler; Sayaka Inoue; Daniel W Bayless; Taehong Yang; Adarsh Tantry; Chung-Ha Davis; Nicole Y Leung; Srinivas Parthasarathy; Grace Wang; Maricruz Alvarado; Abbas H Rizvi; Lief E Fenno; Charu Ramakrishnan; Karl Deisseroth; Nirao M Shah Journal: Cell Date: 2022-01-21 Impact factor: 41.582