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TSCAN specifications

Information


Unique identifier OMICS_11871
Name TSCAN
Alternative name Tools for Single Cell ANalysis
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Hongkai Ji

Additional information


https://zhiji.shinyapps.io/TSCAN/

Information


Unique identifier OMICS_11871
Name TSCAN
Alternative name Tools for Single Cell ANalysis
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.10.2
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Hongkai Ji

Additional information


https://zhiji.shinyapps.io/TSCAN/

Publication for Tools for Single Cell ANalysis

TSCAN citations

 (36)
library_books

A geometric approach to characterize the functional identity of single cells

2018
Nat Commun
PMCID: 5904143
PMID: 29666373
DOI: 10.1038/s41467-018-03933-2

[…] ned each cell to a single dominant function, as determined by its closest archetype. We compare our method to five recently proposed methods: Seurat (v2.2), SNNCliq, BackSPIN, single-cell ParTI,, and TSCAN (Supplementary Note ) to predict annotated cell types on the same four datasets (see Methods, Datasets). For the Melanoma dataset, SNNCliq did not terminate after 72 h, after which we stopped th […]

library_books

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

2018
BMC Genomics
PMCID: 5905132
PMID: 29665773
DOI: 10.1186/s12864-018-4649-2

[…] NMI model, on the other hand, serves homogeneous neuronal samples, including single neurons and purified neuron populations. In the era of single cell biology, pseudo-time construction analysis, e.g. TSCAN [], is commonly used to study transcriptome trajectory of cell development, and may be applied also to study neuron maturation []. This analysis, however, is limited by lacking benchmark of matu […]

library_books

Single Cell Computational Strategies for Lineage Reconstruction in Tissue Systems

2018
PMCID: 5924749
PMID: 29713661
DOI: 10.1016/j.jcmgh.2018.01.023

[…] ir connections approximate the geometric shape of the data cloud when laid out in 2 dimensions. Multiple MST algorithms (eg, Spanning-tree Progression Analysis of Density-normalized Events, Monocle1, Tools for Single Cell ANalysis, Waterfall) exist and they differ by their applications on different experimental platforms, and the type and degree of clustering of data that occurs before MST constru […]

library_books

CellCycleTRACER accounts for cell cycle and volume in mass cytometry data

2018
Nat Commun
PMCID: 5809393
PMID: 29434325
DOI: 10.1038/s41467-018-03005-5

[…] han S due to the jump in IdU. The other methods tested resulted in different incorrect orderings. SCUBA49 constructed a G2→S→G0/G1 trajectory and incorporated the M phase cells in the other clusters; TSCAN50 constructed a M→S/G2→G0/G1 trajectory by mixing together G2 and S cells; and Monocle ordered the data as G0/G1→M→G0/G1→G2→S, by ordering M phase cells in the middle of the G0/G1 cluster. Last, […]

library_books

Exploring the Complexity of Cortical Development Using Single Cell Transcriptomics

2018
Front Neurosci
PMCID: 5801402
PMID: 29456488
DOI: 10.3389/fnins.2018.00031

[…] clusters. Pseudotime is another important concept in the computational analysis of single-cell transcriptome, 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 fo […]

library_books

A Tuned RF Duty Cycled Wake Up Receiver with −90 dBm Sensitivity

2017
PMCID: 5795938
PMID: 29286345
DOI: 10.3390/s18010086

[…] mode and waits for an ACK after each transmitted WuPt. This forces NdTx to stop transmitting WuPts immediately after the reception of an ACK. While packet overhead is reduced at the transmitter side, Tscan of the WuRx cannot be further reduced if it must obey the expression in Equation ().The condition guarantees the reception of a WuPt. (1)Tscan≥2TWuPt+2Ttx_rx+Tack where TWuPt is the time slot of […]

Citations

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TSCAN institution(s)
Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
TSCAN funding source(s)
National Institutes of Health (NIH) [R01HG006282]

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