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scmap specifications

Information


Unique identifier OMICS_19142
Name scmap
Interface Web user interface
Restrictions to use None
Input format RDS
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Download


github.png

Maintainer


  • person_outline Vladimir Kiselev

Additional information


https://hemberg-lab.github.io/scRNA.seq.datasets/

Information


Unique identifier OMICS_19142
Name scmap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format RDS
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Download


download.png
github.png

Versioning


No version available

Maintainer


  • person_outline Vladimir Kiselev

Additional information


https://hemberg-lab.github.io/scRNA.seq.datasets/

Publication for scmap

scmap citations

 (4)
library_books

Cell ontology in an age of data driven cell classification

2017
BMC Bioinformatics
PMCID: 5763290
PMID: 29322914
DOI: 10.1186/s12859-017-1980-6

[…] ogy, with results ranked, as for BLAST, using a similarity score.BLAST-like techniques are also being developed to automatically map cell identity between single cell RNAseq experiments. For example, SCMAP [] can map between cell clusters from two different single cell RNAseq analyses, or from clusters in one experiment to single cells in another.Unsupervised clustering of transcriptomic profiles […]

library_books

Cells in experimental life sciences challenges and solution to the rapid evolution of knowledge

2017
BMC Bioinformatics
PMCID: 5763506
PMID: 29322916
DOI: 10.1186/s12859-017-1976-2

[…] are of many controlled vocabularies and ontologies established under the OBO’s umbrella. Tools and database infrastructures are being built to accommodate high-complexity biological knowledge such as scMap to cluster and classify cell types of single-cell information based on the expression level [], or Stemformatics knowledgebase for stem cell derived cell lines []. Managing and processing data i […]

library_books

A genome wide SNP based genetic map and QTL mapping for agronomic traits in Chinese cabbage

2017
Sci Rep
PMCID: 5394690
PMID: 28418033
DOI: 10.1038/srep46305

[…] tion (χ2 test, P < 0.001, d.f. = 2) were excluded. Co-segregating SNP loci were collapsed into bins, and a linkage bin-map was constructed from the recombination bins serving as genetic markers using ScMap software (Novogene Bioinformatics Technology Co. Ltd, Beijing China). The ScMap software used a modified version of the sliding-window approach developed by Huang et al.. […]

library_books

Impaired Glutathione Redox System Paradoxically Suppresses Angiotensin II Induced Vascular Remodeling

2014
PLoS One
PMCID: 4208744
PMID: 25343455
DOI: 10.1371/journal.pone.0108115

[…] from the law of Laplace (in units of force per unit area) as σc = P⋅r/w, where P is pressure, r is the lumen radius of the artery, and w is the wall thickness. We measured σc in regard to both mean (σcMAP) and systolic blood pressures (σcSAP). […]

Citations

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scmap institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

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