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 |