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seAMLess

A single cell transcriptomics based deconvolution pipeline for Leukemia

https://github.com/eonurk/seamless

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary

Keywords

aml deconvolution venetoclax
Last synced: 6 months ago · JSON representation

Repository

A single cell transcriptomics based deconvolution pipeline for Leukemia

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
aml deconvolution venetoclax
Created almost 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.Rmd 

---
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

Owner

  • Name: Onur Karakaslar
  • Login: eonurk
  • Kind: user
  • Location: Leiden

Featuring random thoughts

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 1
  • Push event: 5
  • Pull request event: 2
Last Year
  • Issues event: 1
  • Issue comment event: 1
  • Push event: 5
  • Pull request event: 2

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 2
  • Total pull requests: 2
  • Average time to close issues: 8 months
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Redmar-van-den-Berg (1)
  • hsiaoyi0504 (1)
Pull Request Authors
  • Redmar-van-den-Berg (3)
Top Labels
Issue Labels
documentation (1) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 505 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: seAMLess

A Single Cell Transcriptomics Based Deconvolution Pipeline for Leukemia

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 505 Last month
Rankings
Forks count: 17.8%
Stargazers count: 28.5%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 39.5%
Downloads: 86.2%
Maintainers (1)
eonurkara@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • Biobase * imports
  • ggplot2 * imports
  • ggtern * imports
  • randomForest * imports
  • MuSiC * suggests
  • seAMLessData * suggests
  • xbioc * suggests