A Single Cell Transcriptomics Based Deconvolution Pipeline for Leukemia

Documentation for package ‘seAMLess’ version 0.1.1

cli	Command Line Interface for seAMLess
exampleTCGA	TCGA-LAML bulk RNA-seq data downloaded from GDC
exampleTCGAmeta	TCGA-LAML example data meta file downloaded from GDC
grch38	Grch38
minRes	A minimal seAMLess result list object
seAMLess	Given the count matrices of bulk-RNA samples, this function deconvolutes each sample into its cell types using a healthy BM reference, and calculates the sample's in vitro resistance to Venetoclax.
ternaryPlot	Given the immune compositions (ICs) of bulk-RNA samples, this function creates a ternary plot similar to ALOT tube from EuroFlow analysis and Figure 1E of our paper.
venoModel	Trained RF model on Venetoclax Resistance
verboseFn	verboseFn
wrangleMat	removes ERCC peaks and duplicated genes