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Oscope specifications


Unique identifier OMICS_09839
Name Oscope
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 0.99.1
Stability Stable
EBSeq, cluster, testthat, BiocParallel
Maintained Yes


No version available


  • person_outline Ning Leng

Publication for Oscope

Oscope citations


Exploring the Complexity of Cortical Development Using Single Cell Transcriptomics

Front Neurosci
PMCID: 5801402
PMID: 29456488
DOI: 10.3389/fnins.2018.00031

[…] iptome, which estimates the cells' progress through the transition. The computational tools like TSCAN (Ji and Ji, ), Monocle (Trapnell et al., ), Waterfall (Shin et al., ), Sincell (Julia et al., ), Oscope (Leng et al., ), and Wanderlust (Bendall et al., ) provide in silico defined pseudotime for each single-cell during the cell fate transition.To gain the first glimpse into the characteristic of […]


Single cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

PLoS Biol
PMCID: 5746276
PMID: 29240790
DOI: 10.1371/journal.pbio.2004050

[…] from unstressed or stressed cells from all other phases; stressed and unstressed cells were analyzed separately unless otherwise noted. All cell classifications from this work are summarized in .The Oscope [] R package version 1.4.0 was used to identify oscillatory genes in the set of unstressed cells. Oscope first filtered transcripts using the function CalcMV and analyzed only those having a mi […]


Single Cell Transcriptomics Bioinformatics and Computational Challenges

Front Genet
PMCID: 5030210
PMID: 27708664
DOI: 10.3389/fgene.2016.00163

[…] a binary tree, which can then be used to model gene expression dynamics (Marco et al., ). However, one drawback of SCUBA is that it requires data with temporal features. Free from such a requirement, Oscope is another method to infer oscillatory genes among single cells collected from a single tissue (Leng et al., ). It hypothesizes that these cells represent distinct states according to an oscill […]


Design and computational analysis of single cell RNA sequencing experiments

Genome Biol
PMCID: 4823857
PMID: 27052890
DOI: 10.1186/s13059-016-0927-y

[…] genes that follow the same oscillatory process need not have similar transcriptional profiles. Two genes with an identical frequency that are phase shifted, for example, will have little similarity. Oscope was developed to enable the identification and reconstruction of oscillatory trajectories []. Like other pseudotemporal reconstruction algorithms, Oscope capitalizes on the fact that cells from […]

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Oscope institution(s)
Department of Statistics, University of Wisconsin–Madison, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA; Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI, USA; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, WI, USA

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