Function reference • mastR

All functions
`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
`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
`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
`plotPCAbiplot()`	Single PCA plot function
`plot_diagnostics()`	plot diagnostics before and after `process_data()`
`plot_mean_var()`	plot Mean-variance trend after voom and after final linear fit
`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

Reference

All functions