# Markers Automated Screening Tool in R

## Documentation for package ‘mastR’ version 1.13.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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.
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
de_analysis | DE analysis pipeline
filter_subset_sig | Filter specific cell type signature genes against other subsets.
filter_subset_sig-method | Filter specific cell type signature genes against other subsets.
get_degs | Get differentially expressed genes by comparing specified groups
get_degs-method | Get differentially expressed genes by comparing specified groups
get_de_table | Get DE analysis result table(s) with statistics
get_de_table-method | Get DE analysis result table(s) with statistics
get_gsc_sig | Collect genes from MSigDB or provided GeneSetCollection.
get_gsc_sig-method | 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
gls2gsc-method | 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-method | 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
process_data-method | process data
pseudo_samples | Aggregate single cells to pseudo-samples according to specific factors
pseudo_samples-method | Aggregate single cells to pseudo-samples according to specific factors
pseudo_sample_list | Split cells according to specific factors
remove_bg_exp | Remove markers with high signal in background data.
remove_bg_exp-method | 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_boxplot-method | Boxplot of median expression or scores of signature
sig_gseaplot | Visualize GSEA result with input list of gene symbols.
sig_gseaplot-method | Visualize GSEA result with input list of gene symbols.
sig_heatmap | Heatmap original markers and screened signature
sig_heatmap-method | Heatmap original markers and screened signature
sig_rankdensity_plot | Plot rank density
sig_rankdensity_plot-method | Plot rank density
sig_scatter_plot | Scatter plot of signature for specific subset vs others
sig_scatter_plot-method | 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