spatialHeatmap-package | spatialHeatmap Spatial Heatmap, Matrix Heatmap, Network |
adj_mod | Compute Adjacency Matrix and Identify Modules |
aggr_rep | Aggregate "Sample__Condition" Replicates in Data Matrix |
aSVG.remote.repo | A list of URLs of remote aSVG repos |
attribute | Methods for S4 class 'SVG' |
attribute-method | Methods for S4 class 'SVG' |
attribute<- | Methods for S4 class 'SVG' |
attribute<--method | Methods for S4 class 'SVG' |
cluster_cell | Cluster single cells or combination of single cells and bulk |
cmb | Methods for S4 class 'SVG' |
cmb-method | Methods for S4 class 'SVG' |
cocluster | Co-clustering bulk and single cell data |
coclus_opt | Optimization of co-clustering bulk and single cell data |
com_factor | Combine Factors in Targets File |
coordinate | Methods for S4 class 'SVG' |
coordinate-method | Methods for S4 class 'SVG' |
coordinate<- | Methods for S4 class 'SVG' |
coordinate<--method | Methods for S4 class 'SVG' |
covis | Co-visualizing spatial heatmaps with single cell embedding plots |
covis-method | Co-visualizing spatial heatmaps with single cell embedding plots |
custom_shiny | Create Customized Shiny App of Spaital Heatmap |
deg.table | A table of differentialy-expressed genes (DEGs) detected by different methods |
deg_ovl | Plot Overlap of Spatially-Enriched Genes Across Methods |
desired_bulk_shiny | Co-clustering bulk and single cell data |
dimension | Methods for S4 class 'SVG' |
dimension-method | Methods for S4 class 'SVG' |
dimension<- | Methods for S4 class 'SVG' |
dimension<--method | Methods for S4 class 'SVG' |
edit_tar | Edit Targets Files |
filter_asg | Co-clustering bulk and single cell data |
filter_cell | Co-clustering bulk and single cell data |
filter_data | Filter the Data Matrix |
graph_line | Plot Gene Expression Profiles in a Data Frame |
length-method | Methods for S4 class 'SVG' |
lis.deg.up.down | A nested list of differentialy-expressed genes (DEGs) detected by different methods |
manual_group | Add manual cell group labels to SingleCellExperiment |
matrix_hm | Matrix Heatmap |
names | Methods for S4 class 'SVG' |
names-method | Methods for S4 class 'SVG' |
names<--method | Methods for S4 class 'SVG' |
network | Visualize a Target Assayed Item in a Network Graph |
norm_cell | Normalizing single cell data |
norm_data | Normalize Sequencing Count Matrix |
opt_bar | Bar plots of co-clustering optimization results. |
opt_setting | Bar plots of co-clustering optimization results. |
opt_violin | Violin plots of co-clustering validation results |
plot_dim | Embedding plots of single cells/bulk tissues after co-clustering |
process_cell_meta | Processing single cell RNA-seq count data |
qc_cell | Quality control in single cell data |
raster | Methods for S4 class 'SVG' |
raster-method | Methods for S4 class 'SVG' |
raster<- | Methods for S4 class 'SVG' |
raster<--method | Methods for S4 class 'SVG' |
read_cache | Read R Objects from Cache |
read_fr | Import Data from Tabular Files |
read_hdf5 | Read Data from the Shiny App Database |
read_svg | Parsing annotated SVG (aSVG) files |
reduce_dim | Reducing dimensionality in count data |
reduce_rep | Reduce sample replicates |
refine_asg | Co-clustering bulk and single cell data |
refine_cluster | Refine single cell clusters |
return_feature | Return aSVG Files Relevant to Target Features |
save_cache | Save R Objects in Cache |
shiny_shm | Integrated Shiny App |
spatialHeatmap | spatialHeatmap Spatial Heatmap, Matrix Heatmap, Network |
spatial_enrich | Identify Spatial Feature-Specifcally Expressed Genes |
spatial_hm | Plot Spatial Heatmaps |
spatial_hm-method | Plot Spatial Heatmaps |
submatrix | Subset Target Assayed Items and Their Nearest Neighbors |
sub_ft | Methods for S4 class 'SVG' |
sub_ft-method | Methods for S4 class 'SVG' |
SVG | The SVG class for storing annotated SVG (aSVG) instances |
svg | Methods for S4 class 'SVG' |
SVG-class | The SVG class for storing annotated SVG (aSVG) instances |
svg-method | Methods for S4 class 'SVG' |
svg<- | Methods for S4 class 'SVG' |
svg<--method | Methods for S4 class 'SVG' |
SVGMethods | Methods for S4 class 'SVG' |
tar_ref | Subset Target Data for Spatial Enrichment |
true_bulk | Assign true bulk to cells in 'colData' slot. |
update_feature | Update aSVG Spatial Features |
write_hdf5 | Construct Database for the Shiny App |
[-method | Methods for S4 class 'SVG' |
[<--method | Methods for S4 class 'SVG' |