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chevron_left Dimensionality reduction Cell lineage and pseudotime inference Normalization Quality control Gene filtering scRNA-seq data integration Differential expression detection Clustering Data visualization chevron_right
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SCell specifications

Information


Unique identifier OMICS_11545
Name SCell
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data SCell accepts as input a matrix of raw gene counts with genes as rows and cells as columns.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Aaron Diaz <>

Publication for SCell

SCell in publications

 (26)
PMCID: 5802385
PMID: 29430484
DOI: 10.21769/BioProtoc.2710

[…] keys on the keyboard (selection → restore).from the menu bar select: analyze → set measurements. pick ‘area’ (represents a number of pixels, n) and ‘integrated density’ (sum intensity for the cell, scell). press ‘ok’.to obtain numeric values press ‘ctrl’ + ‘m’ (analyse → measure). record the result in excel.repeat throughout the entire data set for both channels keeping the same roi.repeat […]

PMCID: 5762646
PMID: 29322363
DOI: 10.1186/s11671-017-2419-8

[…] package{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {i}_{\mathrm{pristine}}={s}_{\mathrm{cell}}\times {a}_e\times {e}^2\times \exp \frac{-{b}_e}{e} $$\end{document}ipristine=scell×ae×e2×exp−bee71\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathr […]

PMCID: 5726470
PMID: 28992063
DOI: 10.1093/dnares/dsx026

[…] occurs only in s. bayanus cbs 380 and s. uvarum cbs 395. we were unable to find homologs in spite of extensive search in the literature and databases. also, cox1i4α, well known as coding for he i-scell with a laglidadg motif, was not identified in any other saccharomyces but s. cerevisiae. unlike cox1i4γ it can be found in less related species from the saccharomyces/kluyveromyces complex […]

PMCID: 5431057
PMID: 28465615
DOI: 10.1038/s41598-017-01454-4

[…] droplets (supplementary fig.  ). as a last step, the signals of cells in each droplet are located within the droplet occurence dataset (supplementary fig. ). within these sequences, the cell signal (scell) is filtered by a triangular convolution window of length n with the kernel (1, 2, 3, … n …, 3, 2, 1) (supplementary fig. ). the length n of the kernel should be large enough to filter […]

PMCID: 5336129
PMID: 28218668
DOI: 10.3390/s17020395

[…] of cells in tier tk is: (6)num(tk)=numk=2πγk_nr = 2πrcosδrrr, actually, it is an integer no smaller than numk. because: (7)hk_n=r−rsinδrr and: (8)hk_w=r then, we can get the area of each cell is: (9)scell_k=r2πγk_n(2πγk_w⋅hk_w−2πγk_n⋅hk_n), furthermore, a simplified formula is obtained as follows: (10)scell_k=rγk_n(γk_w⋅hk_w−γk_n⋅hk_n), finally, we can get: […]


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SCell institution(s)
Department of Neurological Surgery, UCSF, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA; Veterans Affairs Medical Center, San Francisco, CA, USA
SCell funding source(s)
This work has been supported by UCSF-CTSI UL1 TR000004; a Shurl and Kay Circa Foundation Research Grant; a Damon Runyon Cancer Research Foundation postdoctoral fellowship (DRG-2166-13); a VA award 5I01 BX000252; and by NIH awards U01 MH105989 and R01NS075998.

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