README.rmd

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output: github_document
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# deconvR : Simulation and Deconvolution of Omic Profiles

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<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.](http://bioinformatics.mdc-berlin.de/deconvR/)