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Dsection specifications

Information


Unique identifier OMICS_15400
Name Dsection
Interface Application programming interface
Restrictions to use None
Input data Expression data, Proportion data
Output data Output table is formatted so that a triplet of columns (E = "Expression estimate", S = "Standard deviation", N = "Sample size") represents one cell-type and experimental condition pair.
Computer skills Advanced
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Timo Erkkila <>

Information


Unique identifier OMICS_15400
Name Dsection
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Timo Erkkila <>

Dsection in publications

 (7)
PMCID: 5648148
PMID: 29049343
DOI: 10.1371/journal.pone.0186167

[…] and in addition, more accurate identification of differentially expressed genes when compared to other widely known methods for blind decomposition of heterogeneous gene expression data such as dsection and the nonnegative matrix factorization (nmf) algorithms. matlab implementation of the proposed smc algorithm is available to download at https://github.com/moyanre/smcgenedeconv.git., […]

PMCID: 5470467
PMID: 28489035
DOI: 10.3390/s17051077

[…] belongs to [0, dspherical, maxdistorted spherical bubble if lchord,j belongs to [dspherical, max, ddistorted, max]caps bubbles if lchord,j belongs to [ddistorted, max, dcaps,max]slugs if lchord,j>dsection where the group limits are defined by the following expressions:(5)dspherical, max=5.65 drefnμf; ddistorted,max=4 dref; dcaps,max=40 dref where the reference bubble diameter dref is taken […]

PMCID: 5390918
PMID: 28469415
DOI: 10.1177/1177932216687545

[…] multiple types of prediction methods to address some of the limitations., the complexity of immune system was also addressed in the paper by dozmorov et al. the authors compare 2 methods, cssam and dsection, for detection of cell type–specific differential expression by analyzing rna-seq data obtained from a heterogeneous mixture of immune cells of healthy individuals and patients diagnosed […]

PMCID: 5073979
PMID: 27766949
DOI: 10.1186/s12859-016-1226-z

[…] gene expression measures, and 2) either the cell signatures (first approach), or cell proportions (second approach)., two algorithms addressing the second approach have been published (cssam, dsection) [, ]. the cssam approach uses heterogeneous observations as outcomes in a linear regression model, and the measured cell proportions as predictors. two regressions, one per study group […]

PMCID: 4599594
PMID: 26512198
DOI: 10.4137/BBI.S29470

[…] in peripheral blood. to better understand the contribution of different cell types in sle pathogenesis, we applied the two methods in cell-type-specific differential expression analysis, cssam and dsection, to identify cell-type-specific gene expression differences in heterogeneous gene expression measures obtained using rna-seq technology. we identified b-cell-, monocyte-, […]


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