title: SCell: integrated analysis of single-cell RNA-seq data.
abstract: Analysis of the composition of heterogeneous tissue has been greatly enabled by recent developments in single-cell transcriptomics. We present SCell, an integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large ensembles of single-cell RNA-seq datasets. SCell is open source, and implemented with an intuitive graphical interface. Scripts and protocols for the high-throughput pre-processing of large ensembles of single-cell, RNA-seq datasets are provided as an additional resource.
  
  
  
  Binary executables for Windows, MacOS and Linux are available at http://sourceforge.net/projects/scell, source code and pre-processing scripts are available from https://github.com/diazlab/SCellSupplementary information: Supplementary data are available at Bioinformatics online.
  
  
  
  aaron.diaz@ucsf.edu.
authors.affiliation: Department of Neurological Surgery, UCSF Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
authors.forename: Aaron
authors.initials: A
authors.lastname: Diaz
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
authors.forename: Siyuan J
authors.initials: SJ
authors.lastname: Liu
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
authors.forename: Carmen
authors.initials: C
authors.lastname: Sandoval
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
authors.forename: Alex
authors.initials: A
authors.lastname: Pollen
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
authors.forename: Tom J
authors.initials: TJ
authors.lastname: Nowakowski
authors.affiliation: Department of Neurological Surgery, UCSF Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Lim
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
authors.forename: Arnold
authors.initials: A
authors.lastname: Kriegstein
mesh_terms: D059014:High-Throughput Nucleotide Sequencing; D012313:RNA; D017423:Sequence Analysis, RNA; D059010:Single-Cell Analysis; D012984:Software
chemical_list: D012313:RNA