# Quantification of the Tumor Immune contexture from RNA-seq data

## Documentation for package ‘quantiseqr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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