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Protocols

CellMix specifications

Information


Unique identifier OMICS_07121
Name CellMix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Requirements
methods, pkgmaker, NMF, csSAM, registry, stats, stringr, GSEABase, Biobase
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Renaud Gaujoux

Publication for CellMix

CellMix citations

 (25)
call_split

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

2018
PLoS One
PMCID: 5832224
PMID: 29494600
DOI: 10.1371/journal.pone.0193067
call_split See protocol

[…] hold the name of a probe or gene. The software also allows the retrieving of NCBI GEO data sets directly.To compare our deconvolution approach to existing and published methods, we used the R package CellMix [, ]. The partial deconvolution methods lsfit and qprog implemented in CellMix provide estimates of cell-type proportions in a mixed sample given the expression profiles of the pure cell types […]

library_books

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men

2018
PLoS One
PMCID: 5831037
PMID: 29489876
DOI: 10.1371/journal.pone.0192947

[…] ed. Ensembl IDs were converted to gene symbols using BioMart (v2.26.1, Ensembl Genes 86, Dataset version GRCh37.p13) [, ]. The composition of the three main white blood cell types was estimated using CellMix package (v1.6) [] that applies a deconvolution method using gene expression profiles of blood cell types []. […]

library_books

Development of multivariable models to predict change in Body Mass Index within a clinical trial population of psychotic individuals

2017
Sci Rep
PMCID: 5677086
PMID: 29116126
DOI: 10.1038/s41598-017-15137-7

[…] probes and 153 individuals. 40 sex fails identified based on XIST expression were removed, leaving 108 individuals with BMI data, baseline expression data and genetic data (Supplementary Figure ).The CellMix package within R with a pre-determined list of blood cell type markers estimated enrichment for lymphocytes, monocytes and neutrophils. Principal components within the expression data were gen […]

library_books

Genetic variation and gene expression across multiple tissues and developmental stages in a non human primate

2017
Nat Genet
PMCID: 5714271
PMID: 29083405
DOI: 10.1038/ng.3959

[…] tissue using available references for these tissues. For brain tissues, gene signatures were obtained from Zhang et al.; for blood, cell type specific markers were taken from datasets built into the CellMix package. Cell type composition for each tissue was evaluated using the CellMix R package. […]

library_books

Genome wide expression and response to exposure based psychological therapy for anxiety disorders

2017
PMCID: 5611743
PMID: 28850109
DOI: 10.1038/tp.2017.177

[…] Cell-type proportions (lymphocyte, neutrophils and monocytes) were estimated using deconvolution methods implemented in CellMix based on previously reported whole blood cell composition values. Change in lymphocyte, neutrophil and monocyte proportions were calculated for pre- to post treatment, and pre-treatment to fol […]

library_books

Cell type deconvolution from DNA methylation: a review of recent applications

2017
Hum Mol Genet
PMCID: 5886462
PMID: 28977446
DOI: 10.1093/hmg/ddx275

[…] entified, the DNAm data are largely forward compatible, allowing integration of past and future studies. Gene expression based deconvolution is also possible for cell-type resolution. Methods include CellMix () and CIBERSORT () for deconvolution of tissue expression profiles, as well as VoCAL () and ImmQuant () for inferring immune cell-type composition from expression data. These applications hav […]

Citations

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CellMix institution(s)
Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa; School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Ireland

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