StemID statistics

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Citations per year

Citations chart

Popular tool citations

chevron_left Cell lineage and pseudotime inference Stem cell prediction Rare cell prediction chevron_right
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Tool usage distribution map

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Associated diseases

Associated diseases


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StemID specifications


Unique identifier OMICS_17165
Name StemID
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Alexander van Oudenaarden <>

Publication for StemID

StemID in pipeline

PMCID: 5092539
PMID: 27693023
DOI: 10.1016/j.cels.2016.09.002

[…] resulted in more complex single-cell libraries with more differentially expressed genes between cell types (f)., to investigate whether we could detect the expected pancreatic cell types, we used stemid, an approach we developed for inferring the existence of stem cell populations from single-cell transcriptomic data (). stemid calculates all pairwise cell-to-cell distances (1 − pearson […]

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StemID in publications

PMCID: 5918840
PMID: 29539434
DOI: 10.1016/j.stemcr.2018.02.005

[…] cells can be generated from cultured human pancreatic ductal tissue (, , , ). we recently showed that in silico analysis of single-cell transcriptome profiles of human adult pancreatic cells using a stemid algorithm predicts a distinct subpopulation of ductal cells with multipotential differentiation potential (). in mice, the existence of postnatal endocrine progenitors within the pancreatic […]

PMCID: 5605721
PMID: 28951822
DOI: 10.1016/j.molmet.2017.06.021

[…] pancreatic lineages as well as neural lineages . in agreement, grün et al. identified two ductal cell clusters with a high multipotency score in the adult human pancreas using their newly developed stemid algorithm to detect potential stem cell populations within heterogeneous cell populations . the inferred pancreatic lineage tree implies that distinct subtypes of ductal cells give rise […]

PMCID: 5461595
PMID: 28569836
DOI: 10.1038/ncomms15599

[…] as to reconstruct cell-lineage trajectories from time-course data. in this regard, scent differs substantially from other single-cell algorithms like monocle, mpath, scuba, diffusion pseudotime or stemid, in that it uses single-cell entropy to independently order single cells in pseudo-time (that is, differentiation potency), without the need for feature selection or clustering., a pluripotent […]

PMCID: 5352226
PMID: 28296636
DOI: 10.7554/eLife.20488.034

[…] lineage or distance relationship among the putative types is immediately apparent from this clustering. analysis of this data with other recent methods such as monocle and monocle2 (), tscan (), and stemid () did not clearly reconstruct lineage or infer key genes regulating transitions ( – bottom, ). monocle2 () produces a tree with complex branching, but sox2+ progenitors and dcx+ […]

PMCID: 5092539
PMID: 27693023
DOI: 10.1016/j.cels.2016.09.002

[…] mellitus., • single-cell sequencing of human pancreas allows in silico purification of cell types • we provide cell-type-specific genes, transcription factors, and cell-surface markers • stemid finds outlier populations of acinar and beta cells • cd24 and tm4sf4 function as two markers to enrich for alpha and beta cells , single-cell sequencing of human pancreas allows in silico […]

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StemID institution(s)
Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht, Netherlands; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Department of Medicine, Section of Nephrology and Section of Endocrinology, Leiden University Medical Center, Leiden, Netherlands; Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
StemID funding source(s)
Supported by European Research Council Advanced Grant ERC-AdG 294325-GeneNoiseControl, a Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) Vici award, the DON Foundation, and the Dutch Research Foundation.

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