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<!-- is generated from README.Rmd. Please edit that file --> # deconvR : Simulation and Deconvolution of Omic Profiles [![R-CMD-check](]( [![codecov](]( [![](]( <!-- badges: start --> <!-- badges: end --> <img src="deconvR_logo.png" align="left" alt="logo" width="300" style = "border: none; float: center ;"> The **deconvR** package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference signature profiles and a user-selected model (non-negative least squares,quadratic programming, support vector regression, or robust linear regression). Users can directly use their reference atlas or, create an expended version of their reference atlas using `findSignatures`. Additionnaly, they can also use the reference atlas provided within the package, which contains cell-type specific methylation values. Another option is to simulate bulk signatures of bulk samples using `simulateCellMix`. And finally, we included `BSmeth2Probe` function along with the `Illumina Methylation EPIC B5 Manifest` probe IDs, to be used to map methylation data to respective probe IDs. ## Installation The deconvR package can be installed from Bioconductor: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("deconvR") ``` You can also install the development version of **deconvR** directly from Github: ``` r remotes::install_github("BIMSBbioinfo/deconvR") ``` ## How to Use deconvR User who wish to expand their own reference atlas can use `findSignatures` function. `atlas` is the signature matrix to be extended and `samples` the new data to be added to the signature matrix. `atlas` and `samples` are compliant with the function requirements. After providing appropriate `atlas` format, users can create `samples` using `simulateCellMix` function. You can get more information about **deconvR** from [here.](