Wishbone statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left scRNA-seq data visualization Data analysis Cell lineage and pseudotime inference Expression pattern detection chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

Wishbone specifications


Unique identifier OMICS_17996
Name Wishbone
Software type Package/Module
Interface Command line interface
Input data Some multidimensional single-cell data, mass cytometry or RNA-seq data.
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes



Add your version


  • person_outline Dana Pe’er <>

Additional information

https://github.com/ManuSetty/wishbone; A registration is needed to access to tools.

Publication for Wishbone

Wishbone in publications

PMCID: 5924749
PMID: 29713661
DOI: 10.1016/j.jcmgh.2018.01.023

[…] major structures and progressive trends in the data. multiple such embedding approaches have been adopted for single-cell data analysis, including diffusion maps used in various algorithms such as wishbone,, local linear embedding used in selective locally linear inference of cellular expression relationships, and multidimensional scaling and mapper in sctda. adoption of nonlinear embedding […]

PMCID: 5483230
PMID: 28602650
DOI: 10.1016/j.cub.2017.05.028

[…] method, monocle [], detected no branching of the developmental trajectory (e), despite reliably ordering cells by well-known developmental markers (b). alternative pseudotime methods, scuba [] and wishbone [], also did not consistently identify branching (c and s1d). in addition, no clear segregation of cells into the primary lineages (prestalk and prespore) could be detected in correlation […]

PMCID: 5860029
PMID: 28582478
DOI: 10.1093/bioinformatics/btx325

[…] of methods have been proposed that can reconstruct differentiation trajectories, given snapshot data of individual cells in different stages of the differentiation process, such as monocle (), wishbone (), diffusion pseudotime (dpt) (), slicer () and tscan (). given a ‘root’ cell as a starting point, most of these methods can also calculate an ordering of the cells (pseudotime) based […]

To access a full list of publications, you will need to upgrade to our premium service.

Wishbone institution(s)
Department of Biological Sciences, Department of Systems Biology, Columbia University, New York NY, USA; Department of Immunology, Weizmann Institute of Science, Rehovot, Israel; Department of Mathematics, University of British Columbia, Vancouver, BC, Canada; Biological Services Unit, Weizmann Institute of Science, Rehovot, Israel; Department of Pathology, Stanford University, Stanford, CA, USA
Wishbone funding source(s)
Supported by NSF MCB-1149728, NIH DP1- HD084071, NIH R01CA164729; by a Packard Fellowship for Science and Engineering; by David and Fela Shapell Family Foundation INCPM Fund, the WIS staff scientists grant from the Nissim Center, for the Development of Scientific Resources, and ISF 1184/15.

Wishbone review

star_border star_border star_border star_border star_border
star star star star star

jingyao zeng

star_border star_border star_border star_border star_border
star star star star star
very good!