Quantification of the Tumor Immune contexture from RNA-seq data

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Documentation for package ‘quantiseqr’ version 1.15.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

check_signature	Check the signature matrix
dataset_racle	An exemplary dataset with samples from four patients with metastatic melanoma
DClsei	Solve Least Squares with Equality and Inequality Constraints (LSEI) problem
DCrr	Perform robust regression
eset_to_matrix	Convert a 'Biobase::ExpressionSet' to a gene-expression matrix.
extract_ti_from_se	Extract tumor immune quantifications
fixMixture	Format the mixture matrix before deconvolution
get_densities	Scale deconvoluted cell fractions to cell densities
makeQN	Perform quantile normalization of expression data
mapGenes	Rename gene symbols before deconvolution
quantiplot	Plot the information on the tumor immune contexture
quanTIseq	Run quanTIseq deconvolution
quantiseqr-pkg	quantiseqr package
quantiseq_helper	Helper functions for quanTIseq
run_quantiseq	Run the quanTIseq algorithm
se_to_matrix	SummarizedExperiment to matrix
ti_quant_sim1700mixtures	quanTIseq output for the simulation data of 1700 mixtures for RNA-seq data