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Documentation was updated (run_spectra_from_matrix)
Description file / examples updated / etc. for CRAN compatibility
Gene filtering bug in run_spectra_from_matrix was fixed
process_gene_sets_from_KEGG can be run on a vector of gene symbols (no object needed anymore)
Create_references was fixed to not use the variable "sample" within the subset function which caused issues when object$sample was a column in the object
