https://github.com/eonurk/seamless

A single cell transcriptomics based deconvolution pipeline for Leukemia
https://github.com/eonurk/seamless

aml deconvolution venetoclax

Last synced: 5 months ago
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A single cell transcriptomics based deconvolution pipeline for Leukemia

• Host: GitHub
• URL: https://github.com/eonurk/seamless
• Owner: eonurk
• Created: 2022-04-15T18:10:32.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2024-12-19T16:34:26.000Z (over 1 year ago)
• Last Synced: 2025-10-10T18:14:48.886Z (5 months ago)
• Topics: aml, deconvolution, venetoclax
• Language: R
• Homepage: https://www.nature.com/articles/s41698-024-00596-9
• Size: 93 MB
• Stars: 2
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd

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README

          
---

title: "seAMLess"

output: github_document

---

## Overview

`seAMLess` is a wrapper function which deconvolutes bulk Acute Myeloid Leukemia (AML) RNA-seq samples with a healthy single cell reference atlas.

![https://eonurk.github.io/cinaR/articles/cinaR.html](man/figures/Figure1-A.png)

## Installation

[![CRAN version](https://www.r-pkg.org/badges/version/seAMLess)](https://cran.r-project.org/package=seAMLess)

[![CRAN download](https://cranlogs.r-pkg.org/badges/seAMLess?color=orange)](https://cran.r-project.org/package=seAMLess?color=orange)

```{r, eval=FALSE}

# CRAN mirror

install.packages("seAMLess")

```

### Development version

To get bug fix and use a feature from the development version: 

```{r, eval=FALSE}

# install.packages("devtools")

devtools::install_github("eonurk/seAMLess")

```

### Bioconda

![Bioconda version](https://anaconda.org/bioconda/r-seamless/badges/version.svg)

![Bioconda download](https://anaconda.org/bioconda/r-seamless/badges/downloads.svg)

`seAMLess` is also available in Bioconda and can be installed via:

```{r, eval=FALSE}

conda install -c bioconda r-seamless 

```

## Usage

```{r warning=FALSE, message=FALSE}

library(seAMLess)

library(xbioc) # required

data(exampleTCGA)

head(exampleTCGA)[, 1:4]

```

```{r warning=FALSE}

# Now run the function

res <- seAMLess(exampleTCGA)

# AML deconvolution

head(res$Deconvolution)[, 1:4]

```

```{r message=FALSE}

# Create ternary plot

ternaryPlot(res)

```

```{r}

# Venetoclax resistance

res$Venetoclax.resistance[1:4]

```

## Contribution

You can send pull requests to make your contributions.

## Author

- [E Onur Karakaslar](https://eonurk.com)

## License

- GNU General Public License v3.0