debCAM: a bioconductor R package for fully unsupervised deconvolution of complex tissues.
Bioinformatics
; 36(12): 3927-3929, 2020 06 01.
Article
en En
| MEDLINE
| ID: mdl-32219387
ABSTRACT
SUMMARY:
We develop a fully unsupervised deconvolution method to dissect complex tissues into molecularly distinctive tissue or cell subtypes based on bulk expression profiles. We implement an R package, deconvolution by Convex Analysis of Mixtures (debCAM) that can automatically detect tissue/cell-specific markers, determine the number of constituent subtypes, calculate subtype proportions in individual samples and estimate tissue/cell-specific expression profiles. We demonstrate the performance and biomedical utility of debCAM on gene expression, methylation, proteomics and imaging data. With enhanced data preprocessing and prior knowledge incorporation, debCAM software tool will allow biologists to perform a more comprehensive and unbiased characterization of tissue remodeling in many biomedical contexts. AVAILABILITY AND IMPLEMENTATION http//bioconductor.org/packages/debCAM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Proteómica
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2020
Tipo del documento:
Article
País de afiliación:
Estados Unidos