ccle_2_wide             Convert CCLE data from long data to wide data.
ccle_crc_5              RNA-seq TPM data of 5 CRC cell line samples
                        from CCLE.
de_analysis             DE analysis pipeline
DEGs_Group              return DEGs UP and DOWN list based on
                        intersection or union of comparisons
DEGs_RP                 return DEGs UP and DOWN list based on Rank
                        Product
filter_subset_sig       Filter specific cell type signature genes
                        against other subsets.
get_de_table            Get DE analysis result table(s) with statistics
get_degs                Get differentially expressed genes by comparing
                        specified groups
get_gsc_sig             Collect genes from MSigDB or provided
                        GeneSetCollection.
get_lm_sig              Extract specific subset markers from LM7 or/and
                        LM22
get_panglao_sig         Extract immune subset markers from PanglaoDB
                        website.
gls2gsc                 Convert gene-set list into GeneSetCollection
gsc_plot                Make upset plot for given gene sets
im_data_6               RNA-seq TMM normalized counts data of 6 sorted
                        immune subsets.
list_panglao_organs     Show the summary info of available organs in
                        PanglaoDB.
list_panglao_types      Show the summary info of available cell types
                        in PanglaoDB.
lm22                    LM22 matrix for CIBERSORT.
lm7                     LM7 matrix for CIBERSORT.
merge_markers           Merge markers list into one.
msigdb_gobp_nk          Sub-collection of MSigDB gene sets.
nk_markers              NK cell markers combination.
pca_matrix_plot         Make a matrix plot of PCA with top PCs
pca_matrix_plot_init    Make a matrix plot of PCA with top PCs
plot_diagnostics        plot diagnostics before and after
                        'process_data()'
plot_mean_var           plot Mean-variance trend after voom and after
                        final linear fit
plotPCAbiplot           Single PCA plot function
process_data            process data
pseudo_sample_list      Split cells according to specific factors
pseudo_samples          Aggregate single cells to pseudo-samples
                        according to specific factors
remove_bg_exp           Remove markers with high signal in background
                        data.
remove_bg_exp_mat       Remove genes show high signal in the background
                        expression data from markers.
select_sig              select DEGs from multiple comparisons
sig_boxplot             Boxplot of median expression or scores of
                        signature
sig_gseaplot            Visualize GSEA result with input list of gene
                        symbols.
sig_heatmap             Heatmap original markers and screened signature
sig_rankdensity_plot    Plot rank density
sig_scatter_plot        Scatter plot of signature for specific subset
                        vs others
voom_fit_treat          return DGEList containing vfit by limma::voom
                        (if normalize = TRUE) and tfit by limma::treat
