A Single Cell Transcriptomics Based Deconvolution Pipeline for Leukemia.

seAMLess

Overview

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

Installation

# CRAN mirror
install.packages("seAMLess")

Development version

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

# install.packages("devtools")
devtools::install_github("eonurk/seAMLess")

Bioconda

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

conda install -c bioconda r-seamless

Next, install the seAMLessData package inside of R, this will take a few minutes:

install.packages("seAMLessData", repos = "https://eonurk.github.io/drat/")

Usage

library(seAMLess)
library(xbioc) # required

data(exampleTCGA)
head(exampleTCGA)[,1:4]

##                    X TCGA.AB.2856.03A TCGA.AB.2849.03A TCGA.AB.2971.03A
## 1 ENSG00000000003.13                7                9                1
## 2  ENSG00000000005.5                0                1                0
## 3 ENSG00000000419.11              689              661              555
## 4 ENSG00000000457.12              633             1434              855
## 5 ENSG00000000460.15              372             1211              519
## 6 ENSG00000000938.11            14712              405             6076

# Now run the function
res <- seAMLess(exampleTCGA)

## >> Human ensembl ids are converted to symbols...

## >> Deconvoluting samples...

## >> Deconvolution completed...

## >> Predicting Venetoclax resistance...

## >> Done...

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

##                  CD14 Mono       GMP     T Cells      pre B
## TCGA.AB.2856.03A 0.1495886 0.7079107 0.022868623 0.00000000
## TCGA.AB.2849.03A 0.0000000 0.0000000 0.000000000 0.00000000
## TCGA.AB.2971.03A 0.5494418 0.4462562 0.002898678 0.00000000
## TCGA.AB.2930.03A 0.0000000 0.4698555 0.000000000 0.00000000
## TCGA.AB.2891.03A 0.0000000 0.6189622 0.018645484 0.01384012
## TCGA.AB.2872.03A 0.0000000 0.9950150 0.000000000 0.00000000

# Create ternary plot
ternaryPlot(res)

# Venetoclax resistance
res$Venetoclax.resistance[1:4]

## TCGA.AB.2856.03A TCGA.AB.2849.03A TCGA.AB.2971.03A TCGA.AB.2930.03A
##        0.5070113        0.3242576        0.6678995        0.3305996

Contribution

You can send pull requests to make your contributions.

Author

• E Onur Karakaslar

License

• GNU General Public License v3.0