Sincell statistics

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chevron_left Clustering Dimensionality reduction scRNA-seq data visualization Cell lineage and pseudotime inference chevron_right
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Sincell specifications

Information


Unique identifier OMICS_09014
Name Sincell
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Requirements
parallel, BiocStyle, ggplot2, biomaRt, knitr, MASS, cluster, fields, reshape2, fastICA, stringr, igraph, R(>=3.0.2), Rcpp(>=0.11.2), entropy, scatterplot3d, TSP, proxy, Rtsne, monocle
Maintained Yes

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Maintainer


  • person_outline Antonio Rausell <>

Publication for Sincell

Sincell in publications

 (5)
PMCID: 5801402
PMID: 29456488
DOI: 10.3389/fnins.2018.00031

[…] 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 for each single-cell during the cell fate transition., to gain the first […]

PMCID: 5818005
PMID: 29361568
DOI: 10.1242/dev.158501

[…] further. stage-specific outliers were screened by pca., principal component and cluster analyses were performed based on log2 fpkm values computed with the bioconductor packages deseq2 (), sincell () or factominer () in addition to custom scripts. t-sne () and diffusion maps were produced with the rtsne (github.com/jkrijthe/rtsne) and destiny () packages, respectively. differential […]

PMCID: 5658171
PMID: 29073251
DOI: 10.1371/journal.ppat.1006678

[…] from the low permissive donor were more heterogeneous than those of the high permissive donor (wilcoxon-rank sum test p-value < 2.2e-16; )., we then explored transcriptional heterogeneity by sincell software for the statistical assessment of cell-state hierarchies developed in our laboratory []. the analysis showed a continuum of transcriptional cell state for both donors, without […]

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

[…] sampling distribution; but with these advantages comes a considerable computational burden. specific implementations that consider subsets of paths can dramatically improve performance []; and sincell provides a general implementation in which various options for dimension reduction and pseudotemporal reconstruction may be specified by a user []., a key assumption that enables […]

PMCID: 3569297
PMID: 23405308
DOI: 10.1128/genomeA.00030-12

[…] phylogenetic analysis of the full-length 16s gene placed the single cell in sar86 subclade iiia, along with two bacs (accession no. ay033328 and af268217); thus, we have named the genome sar86_iiib_sincell1. the genome contains many of the same features observed by dupont et al. (), including an overabundance of tonb receptors, a complete emden-meyerhof-parnas glycolytic pathway, […]


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Sincell institution(s)
Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; University of Lausanne, Lausanne, Switzerland; J Craig Venter Institute, La Jolla, CA

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