Oscope protocols

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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


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  • person_outline Ning Leng <>

Publication for Oscope

Oscope in pipeline

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

[…] 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 […]

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Oscope in publications

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

[…] 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 […]

PMCID: 5797448
PMID: 29404219
DOI: 10.7717/peerj.4327

[…] be used to determine whether the clock is progressing normally., a more sophisticated approach is to assume the presence of rhythms and to infer a cyclical ordering of samples, using methods such as oscope or cyclops (; ). by applying cyclops to transcriptome data from hepatocellular carcinoma, found evidence for weaker or disrupted rhythmicity of several clock genes, as well as genes involved […]

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

[…] not find evidence for the same ymc transcriptome program reported in nutrient-restricted chemostats. first, there was no evidence that rp transcripts are cycling in our dataset. we used the program oscope [] to identify cycling transcripts, which were heavily enriched for cell cycle-regulated mrnas (p = 2e-16, hypergeometric test []) but not rps or transcripts encoding metabolic enzymes (). […]

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

[…] 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 […]

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

[…] al. [] demonstrated nicely that previously masked sub-populations associated with t-cell differentiation are revealed following removal of cell cycle-associated variation., a related approach called oscope [] does not rely on oscillating genes being identified a priori. rather, it was developed to identify and characterize oscillators in snapshot (non temporal) scrna-seq experiments. […]

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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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