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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.