MetaNeighbor specifications


Unique identifier OMICS_19141
Name MetaNeighbor
Alternative name Meta-analysis via Neighbor voting
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A gene-by-sample expression matrix, a numerical vector that indicates the source of each sample, a matrix that indicates the cell type of each sample and a Gene sets of interest provided as a list of vectors or A gene-by-sample expression matrix, a sample metadata table, a vector that lists the names of all cell types and a set of high variance genes.
Output data A vector of AUROC scores representing the mean for each gene set tested, a list containing the AUROC score for each dataset and cell type and a matrix containing the means for each cell type across datasets.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Jesse Gillis
  • person_outline Sara Ballouz
  • person_outline Megan Crow
  • person_outline Anirban Paul
  • person_outline Josh Huang

Publications for Meta-analysis via Neighbor voting

MetaNeighbor citations


Characterizing the replicability of cell types defined by single cell RNA sequencing data using MetaNeighbor

Nat Commun
PMCID: 5830442
PMID: 29491377
DOI: 10.1038/s41467-018-03282-0

[…] The input to MetaNeighbor is a set of genes, a data matrix, and two sets of labels: one set for labeling each experiment and one set for labeling the cell types of interest. For each gene set, the method generates […]


Single cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement

Proc Natl Acad Sci U S A
PMCID: 5798372
PMID: 29343640
DOI: 10.1073/pnas.1717871115

[…] oping LGN, profiling multiple developmental conditions, and characterizing multiple nonneuronal cell types, including astrocytes, microglia, and endothelial cells (, ).We utilized the newly developed MetaNeighbor approach to compare the transcriptional signatures of excitatory neurons, inhibitory neurons, and oligodendrocytes at each postnatal time point in our data with those of the Allen Institu […]

MetaNeighbor institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Program in Neuroscience, Stony Brook University, Stony Brook, NY, USA
MetaNeighbor funding source(s)
Supported by grants from the NIH (5R01MH094705-04 and R01MH109665-01; 1R01MH113005; and 1F32MH114501), by the CSHL Robertson Neuroscience Fund, and by a NARSAD Post-doctoral Fellowship.

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