execute_cibersort | Execute cibersort using Rserve |
expdata_as_df | convert expdaat (as GxS matrix) to tbl_df format |
expdata_as_matrix | convert expdata (as GxS tbl_df) to matrix format |
filter_expdata | helper function to filter gxs expdata more efficiently than... |
filter_genes | Filter GxS expression data to specific list of genes If... |
filter_gxs_expdata | helper function to filter gxs expdata more efficiently than... |
genelist | Selected genes for use with infino models |
load_all_expdata | load several expdata files all at once |
load_expdata | loads expression data in GxS format, with one row per gene &... |
load_lm22_genes | Helper function to load lm22 genes from cibersort_home and... |
merge_expdata | merge expdata dfs together, combining sampleinfo |
prep_expression_matrix | Prepare expression matrix of transcript- or gene-specific... |
rcctils_expression | Gene expression matrices for TILs isolated from RCC patients... |
rcctils_sampleinfo | Sample info for TILs isolated from RCC patients (E-MTAB-5640) |
run_cibersort | Run cibersort on expression data |
run_combat | Run combat to normalize for batch effects |
run_estimate | Run estimate on expression data |
run_pca | run PCA analysis on expression data |
shell | Helper to execute shell commands (linux) |
singleorigin_expression | Gene expression matrices for immune cells isolated from PBMC... |
singleorigin_sampleinfo | Sample info for immune cells isolated from PBMC samples... |
test_cibersort | Test cibersort using one of the expression matrices provided |
transform_cibersort_to_relative | Transform 'Absolute' mode of cibersort results to relative... |
transform_sampleid | Transform sample_id in both expdata & in attributes |
transpose2gxs | Function to transpose an SxG df of expression data into GxS... |
transpose2sxg | Function to transpose an GxS df of expression data into SxG... |
transpose_expdata | helper function to transpose a dataframe of expression data... |
update_sampleinfo | Update sampleinfo affiliated with expdata |
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