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BackSPIN specifications


Unique identifier OMICS_10721
Name BackSPIN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data BackSPIN takes input in CEF format.
Output data It produces an annotated CEF file as output.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Numpy, Scipy, SciKit-learn
Maintained Yes


No version available



  • person_outline Sten Linnarsson <>

Publication for BackSPIN

BackSPIN citations


Exploring the Complexity of Cortical Development Using Single Cell Transcriptomics

PMCID: 5801402
PMID: 29456488
DOI: 10.3389/fnins.2018.00031

[…] et al., ). for the unsupervised clustering, consensusclusterplus r (wilkerson and hayes, ), emcluster (jung et al., ), sc3 (kiselev et al., ), snn-cliq (xu and su, ), scuba (marco et al., ), backspin (zeisel et al., ), and pagoda (fan et al., ) provide methods to identify the subpopulation from the single-cell transcriptome profiles. following clustering, deseq2 (love et al., ), scde […]


Single cell RNA sequencing of the brain

PMCID: 5465230
PMID: 28597408
DOI: 10.1186/s40169-017-0150-9

[…] metrics used for distance-based methods are euclidean distance, pearson, and spearman correlation coefficients [, ]. a recently developed and frequently used hierarchical clustering method is backspin [], which allows for biclustering of both genes and cells. the non-linear unsupervised clustering method, t-sne [], has also been widely used in scrna-seq samples [, ]. clustering methods […]


Single Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

PMCID: 5052454
PMID: 27641957
DOI: 10.1016/j.cels.2016.08.010

[…] could be defined during 1st level clustering. clustering robustness was evaluated as described in (2). additionally, the ap clustering approach was compared with unsupervised clustering by backspin () with good agreement. a t-sne representation of the whole dataset was generated with the same features as used for the ap clustering., a negative binomial regression model was generated […]


Single cell sequencing in stem cell biology

PMCID: 4832540
PMID: 27083874
DOI: 10.1186/s13059-016-0941-0

[…] of stem cells within a dataset is achieved by methods for unbiased clustering and differential gene expression analysis. zeisel et al. [] recently described a biclustering-based algorithm called backspin that increases the accuracy of identifying cell types from single-cell rna-seq data. grun et al. [] developed another algorithm called raceid, which is based on a feature of the single-cell […]

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BackSPIN institution(s)
Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden; Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden

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