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BrainCell specifications


Unique identifier OMICS_19253
Name BrainCell
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of character vectors of human ENSEMBL gene ID.
Output data Brain heatmaps, Cell taxonomy heatmaps, list of matrices with one matrice for each cell type or phenotype.
Output format pdf, R
Operating system Unix/Linux, Mac OS
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Registration required No
Maintained Yes


  • BrainH
  • CellFET
  • CellTax




No version available


  • person_outline Enrico Petretto
  • person_outline Andree Delahaye-Duriez
  • person_outline Michael R. Johnson

Publication for BrainCell

BrainCell citations


Pten and EphB4 regulate the establishment of perisomatic inhibition in mouse visual cortex

Nat Commun
PMCID: 5023968
PMID: 27611660
DOI: 10.1038/ncomms12829

[…] cal neurons, published from the Allen Brain Institute, shows high expression of EphrinB2 in pyramidal neurons; Pten, but not EphB4 is expressed in adult PV cells (see Increased expression of EphB4 in PV cells could account for the reduction in PV to pyramidal inhibitory synapses via increased repulsion between the presynaptic terminals of PV cells and cel […]


Adult Mouse Cortical Cell Taxonomy by Single Cell Transcriptomics

Nat Neurosci
PMCID: 4985242
PMID: 26727548
DOI: 10.1038/nn.4216

[…] ual cortex in adult male mice. The annotated dataset and a single cell gene expression visualization tool are freely accessible via the Allen Brain Atlas data portal ( […]


Comprehensive Identification of Long Non coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination

PLoS Genet
PMCID: 4980008
PMID: 26683846
DOI: 10.1371/journal.pgen.1005669

[…] arge-scale functional lncRNA screens in other cell types. We have presented our datasets and analytical results as online resources freely available to the research community ( (Username: lncRNA; Password: rnaseq). We anticipate that our study will advance the knowledge of this major class of non-coding genes and their potential roles in neurological d […]


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BrainCell institution(s)
Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK; MRC Clinical Sciences Centre, Imperial College London, London, UK; Université Paris 13, Sorbonne Paris Cité, UFR de Santé, Médecine et Biologie Humaine, Paris, France; PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Duke-NUS Medical School, Singapore, Singapore; Neuroscience TA, UCB Pharma, S.A, Brussels, Belgium; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Australia; The Centre for Neural Engineering, The Department of Electrical Engineering, The University of Melbourne, Melbourne, Australia; The Australian Research Council Centre of Excellence for Integrative Brain Function, Melbourne, Australia
BrainCell funding source(s)
This study was supported by the European Union’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 626229 (iGENEE, FP7/2007-2013, Marie Curie Actions, Intra-European Fellowships for Career Development) and under grant agreement no. 602102, by UK Imperial National Institute for Health Research Biomedical Research Centre, the UK Medical Research Council, UCB Pharma, Duke-National University of Singapore, Medical School and the Singapore Ministry of Health.

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