Fig. 1. iS-CellR pipeline overview

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J Exp Bot. 2017;68(17): doi: /jxb/erx352

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Fig. 1. iS-CellR pipeline overview Fig. 1. iS-CellR pipeline overview. iS-CellR is organized into a seven-step process for complete scRNA-seq analysis. ... Fig. 1. iS-CellR pipeline overview. iS-CellR is organized into a seven-step process for complete scRNA-seq analysis. The user can interactively select steps to perform analysis using single-cell data. After uploading, the raw data are filtered and normalized. The normalized data are then subjected to dimensionality reduction for principle component analysis (PCA). Further dimensionality reduction can be performed using t-distributed stochastic neighbour embedding (tSNE). After a clustering step, differentially expressed marker genes can be visualized on cell clusters. The user can also visualize co-expression of two genes simultaneously. Inter-/intra-sample heterogeneity requires the user to upload a file with a list of genes in a two-column format (GeneSet1, GeneSet2). Finally, the user can generate a HTML report containing all results produced or download plots individually Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Bioinformatics, Volume 34, Issue 24, 04 July 2018, Pages 4305–4306, https://doi.org/10.1093/bioinformatics/bty517 The content of this slide may be subject to copyright: please see the slide notes for details.