Cell type proportion is related with certain phenotype or disease (Wei, et al.). Therefore, quantifying cell or tissue proportions is an important problem in bioinformatics.
Here, we proposed a cell type deconvolution evaluating toolkit named ‘Deconer’ to perform comprehensive and systematic analysis for different algorithms.
Deconer consists of 6 main part functions as below.
- Pseudo bulk data generation (including bulk and single cell).
- Stability analysis under different types of noise.
- Rare component analysis.
- Unknown component analysis.
- Comprehensive evaluation metrics.
- Well characterized datasets for deconvolution utilities.
For more information, please see Deconer github page.
library(Deconer)
sessionInfo()
#> R version 4.2.2 (2022-10-31 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 22621)
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] Deconer_1.0.3
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