# Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data

## Documentation for package ‘granulator’ version 1.13.0

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

## Help Pages

benchmark | Regress estimated cell type proportions against the ground truth
bulkRNAseq_ABIS | PBMCs expression profiles (ABIS dataset)
correlate | Pearson correlation of cell type proportions across cell types and methods
deconvolute | Deconvolution from bulk RNAseq
get_decon_methods | Deconvolution methods acronyms
get_TPM | Convert raw counts to TPM
groundTruth_ABIS | PBMCS true cell type proprotions (ABIS dataset)
load_ABIS | Load demo PBMCs deconvolution data
plot_benchmark | Plot benchmarking analysis scores
plot_correlate | Plot of correlations between deconvolution methods
plot_deconvolute | Estimated cell types across methods
plot_proportions | Plot estimated cell type proportions
plot_regress | Plot estimated cell type coefficients against the ground truth
plot_similarity | Plot reference profile similariy matrix
sigMatrix_ABIS_S0 | Signature matrix for deconvolution of PBMCs in 17 cell types
sigMatrix_ABIS_S1 | Signature matrix for deconvolution of PBMCs in 13 cell types
sigMatrix_ABIS_S2 | Signature matrix for deconvolution of PBMCs in 11 cell types
sigMatrix_ABIS_S3 | Signature matrix for deconvolution of PBMCs in 9 cell types