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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Antonio Rausell

Publication for Sincell

Sincell citations

 (5)
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

[…] sis 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 glimpse […]

library_books

Integrated analysis of single cell embryo data yields a unified transcriptome signature for the human pre implantation epiblast

2018
PMCID: 5818005
PMID: 29361568
DOI: 10.1242/dev.158501

[…] 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 expr […]

call_split

Single cell analysis identifies cellular markers of the HIV permissive cell

2017
PLoS Pathog
PMCID: 5658171
PMID: 29073251
DOI: 10.1371/journal.ppat.1006678
call_split See protocol

[…] onor (“poolT12_2”) appeared as an outlier in initial exploratory analyses and was discarded from downstream analyses. Analysis of transcriptional heterogeneity across single cells was performed using Sincell Bioconductor package []. Differential expression analyses used DESeq2 bioconductor package []. Functional enrichment analysis was performed using STRING with default parameters []. An R script […]

library_books

Design and computational analysis of single cell RNA sequencing experiments

2016
Genome Biol
PMCID: 4823857
PMID: 27052890
DOI: 10.1186/s13059-016-0927-y

[…] rlying 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 pseudotemporal […]

library_books

Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa

2013
Genome Announc
PMCID: 3569297
PMID: 23405308
DOI: 10.1128/genomeA.00030-12

[…] A 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, a green-light-a […]

Citations

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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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