SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data

BMC Bioinformatics

Software

Amol Ugale¹  Stefan Lang¹  Eva Erlandsson¹  Göran Karlsson¹  David Bryder¹  Shamit Soneji¹ 

[1] Division of Molecular Hematology, BMC B12, Lund University, Sölvegatan 19, 22184, Lund, Sweden;Lund Stem Cell Center, Lund University, 22184, Lund, Sweden;

关键词: Gene expression;    Single cells;    qRT-PCR;    Webtool;    FACS;    Index sorting;    Visualisation;   

DOI  :  10.1186/s12859-015-0757-z

 received in 2015-03-26, accepted in 2015-08-04,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundSingle cell gene expression assays have become a powerful tool with which to dissect heterogeneous populations. While methods and software exist to interrogate such data, what has been lacking is a unified solution combining analysis and visualisation which is also accessible and intuitive for use by non-bioinformaticians, as well as bioinformaticians.ResultsWe present the Single cell expression visualiser (SCExV), a webtool developed to expedite the analysis of single cell qRT-PCR data. SCExV is able to take any data matrix of Ct values as an input, but can handle files exported by the Fluidigm Biomark platform directly. In addition, SCExV also accepts and automatically integrates cell surface marker intensity values which are measured during index sorting. This allows the user to directly visualise relationships between a single cell gene expression profile and the immunophenotype of the interrogated cell.ConclusionsSCExV is a freely available webtool created to import, filter, analyse, and visualise single cell gene expression data whilst being able to simultaneously consider cellular immunophenotype. SCExV is designed to be intuitive to use whilst maintaining advanced functionality and flexibility in how analyses are performed.

【 授权许可】

CC BY   
© Lang et al. 2015