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deconf specifications


Unique identifier OMICS_21800
Name deconf
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Dirk Repsilber <>

Publication for deconf

deconf citations


Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues

PMCID: 5832224
PMID: 29494600
DOI: 10.1371/journal.pone.0193067

[…] is a more challenging task. for this, no information is available aside from the expression values in multiple heterogeneous tissue samples and an estimate of the number of individual cell types. deconf is an example of this approach using non-negative matrix decomposition []. when testing deconf on artificially mixed test data, we found that its performance was limited even on noise-free […]


An evaluation of methods correcting for cell type heterogeneity in DNA methylation studies

PMCID: 4855979
PMID: 27142380
DOI: 10.1186/s13059-016-0935-y

[…] where confounding does not necessarily result from cell-type mixtures yet is still of concern; many of these rely on some implementation of matrix decompositions (sva [], isva [], deconfounding (deconf) [], and ruv [, ])., although there are numerous similarities between the approaches, there remain some fundamental differences in terms of limitations and performance. an unbiased comparison […]


The meta epigenomic structure of purified human stem cell populations is defined at cis regulatory sequences

PMCID: 4300104
PMID: 25327398
DOI: 10.1038/ncomms6195

[…] of subpopulations within our dataset but did not interpret the specific values within w', rather we focused on the difference between the actual and simulated datasets., utilizing the r package deconf, we varied the matrix rank and estimated the matrices w' and h' such that: (2)v′≈w′h′. the distance between the original dataset v and v' was calculated as the frobenius norm: (3)‖v′−v‖f2=f. […]

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deconf institution(s)
Department of Genetics and Biometry, Research Institute for the Biology of Farm Animals, Dummerstorf, Germany; Bioinformatics Chair, Institute for Biochemistry and Biology at the University of Potsdam, Potsdam-Golm, Germany; Molecular Biology and Human Genetics, University of Stellenbosch, Cape Town, South Africa; Department of Immunology, Max-Planck-Institute for Infection Biology, Berlin, Germany; Department of Immunology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
deconf funding source(s)
Supported by the Grand Challenges in Global Health Project: Grant Number 37772.

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