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

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Documentation for package ‘granulator’ version 1.8.0

• 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