Markers Automated Screening Tool in R

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Documentation for package ‘mastR’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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