Add_AssignVariant | Add_AssignVariant a function to assign variants to edges... |
Add_AssignVariant-redeemR-method | a function to assign variants to edges based on maximum... |
AddDatatoplot_clustering | AddDatatoplot_clustering This prepare the clonal clustering... |
AddDatatoplot_clustering-redeemR-method | AddDatatoplot_clustering This prepare the clonal clustering... |
Add_DepthMatrix | Add_DepthMatrix Optional, add a matrix with same dimension... |
Add_DepthMatrix-redeemR-method | Add_DepthMatrix Optional, add a matrix with same dimension... |
add_derived_profile_info | This is a convinience function, internal borrowed from... |
AddDist | AddDist This add Jaccard, Dice, Jaccard3W distance and stored... |
AddDist_legacy | AddDist_legacy This add Jaccard, Dice, Jaccard3W distance and... |
AddDist_legacy-mitoTracing-method | AddDist_legacy This add Jaccard, Dice, Jaccard3W distance and... |
AddDist-redeemR-method | AddDist This add Jaccard, Dice, Jaccard3W distance and stored... |
AddHemSignature | Function to add hematopoietic signatures from... |
AddsigTag.6.new | AddsigTag.6.new |
AddTree | Add_Tree Optional, if a phylogentic tree object phylo is... |
Add_tree_cut | Add_tree_cut a function to cut tree using assigned variant as... |
Add_tree_cut-redeemR-method | a function to cut tree using assigned variant as... |
AddTree-redeemR-method | Add_Tree Optional, if a phylogentic tree object phylo is... |
ATAC_Wrapper | Wrap Seurat ATAC clustering |
BinaryDist | Compute distances for binary distances |
binomialtest.msig.enrch_deplet | binomialtest.msig.enrch_deplet |
Clone_FinderMarker | Define a function to perform Find marker for top vs bottom... |
ComputeRejectRate | Function to compute the reject rate(The filtering rate in... |
ComputeRejectRate_legacy | Function to compute the reject rate(The filtering rate in... |
convert_mitotracing_redeemR | convert_mitotracing_redeemR |
CountVperCell | Internal function in plot_variant |
Create_mitoTracing | Create_mitoTracing |
Create_redeemR | Create_redeemR |
CV | Internal CV |
CW_mgatk.read | Old Function to read in redeemV outputs It process the data... |
Datatoplots-class | An intermediate S4 class Datatoplots |
DE.gettripple | DE.gettripple |
DepthSummary | Function to summarize the depth (Total that passed Q30) |
df2ProfileMtx | This is a convinience function, internal |
DistObjects-class | An intermediate S4 class Datatoplots |
DoDE | DoDE |
FromDist2Graph | FromDist2Graph From distance object or matrix to graph,... |
Fun.enrich_withFC | Fun.enrich_withFC |
Fun.enrich_withFC.pvalue | Fun.enrich_withFC.pvalue |
GEM_Wrapper | Wrap Seurat RNA clustering |
get_ancestral_nodes | This is a convinience function, internal borrowed from... |
Get_Clonal_Variants | Get_Clonal_Variants |
Getgenenumber | Getgenenumber |
Getpallet2 | Getpallet2 |
gsea_enrichmentheat | gsea_enrichmentheat |
GTSummary | Function to generate GTS summary |
LineageBiasPlot | plot_npSummary to plot the lineage composition |
MakeAllNodes | Define a function make the... |
Make_AnnTable | Make_AnnTable, Make a big dataframe, each row is a cell, each... |
Make_Cells4Nodes | Define a function to make a list, each contains the cell... |
MakeDF4Regress | MakeDF4Regress Define a function to make two dataframe for... |
Make_matrix | Make_matrix This will make the matixies of Cell VS... |
Make_matrix-redeemR-method | Make_matrix This will make the matixies of Cell VS... |
MakeNN | Define a function to make nn list, which can be further used... |
Make_tree | Make_tree This will generate a basic phylogenetic tree |
Make_tree_legacy | Make_tree_legacy This will generate a basic phylogenetic tree |
Make_tree_legacy-mitoTracing-method | Make_tree_legacy This will generate a basic phylogenetic tree |
Make_tree-redeemR-method | Make_tree This will generate a basic phylogenetic tree |
MergeMtx | Function to Merge sparse Matrix |
mitoTracing-class | Legacy function: Major mitoTracing class that store... |
Motifenrich.binom | Motifenrich.binom In house function to compute enrichment... |
Multi_Wrapper | Wrap Seurat Multiomics clustering |
MutationProfile.bulk | Function to plot bulk level mutation signatures |
NN2M | Define a function convert nn list to adjacency matrix that... |
plot_depth | Function to plot the mito depth summary |
plot_depth_legacy | Legacy Function to plot the mito depth summary |
plot_npSummary | plot_npSummary to assess the outputlevel |
plot_variant | Function to plot variant metrics |
plot_variant_legacy | Legacy Function to plot variant metrics |
ProgenyMapping | Define a function to perform single-cell based hard porogeny... |
ProgenyMapping_np | ProgenyMapping_np Define a function to compute network... |
quick_w_cosine | Compute weighted cosine distance |
quick_w_jaccard | Compute weighted jaccard distance |
Reclustering | Function to reclustering a seurat object |
Reclustering_hm | Function to reclustering_hm a seurat object with Harmony |
reconstruct_genotype_summary | This is a function borrowed from... |
redeemR-class | Major redeem class that store clonal-resolved multi-omics |
redeemR.read | Function to read in redeemV outputs |
Run_Lin_regression | Run_Lin_regression |
Run_Lin_regression_poi | Run_Lin_regression_poi Firstly used in... |
Runplot_scale_2 | plot_npSummary to assess the outputlevel vs lineage bias,... |
Runplot_scale_3 | plot_npSummary to assess the outputlevel vs lineage bias,... |
SeuratLSIClustering | SeuratLSIClustering This will use the mito variants for... |
SeuratLSIClustering-redeemR-method | SeuratLSIClustering This will use the mito variants for... |
Show_Consensus | Function to plot consensus mtDNA mutation benchmark |
show-redeemR-method | show This will show the basics of redeemR class |
split_profile | This is a convinience function, internal borrowed from... |
str2vector | This is a convinience function, internal |
Subset_redeemR | Subset_redeemR Subset a redeemR object by selecting a subset... |
Tomerge.col | Tomerge.col |
Tomerge_v2 | Tomerge_v2 |
Translate_RNA2ATAC | Function to translate the RNA barcode into ATAC barcode and... |
Translate_simple_ATAC2RNA | Translate_simple_ATAC2RNA |
Translate_simple_RNA2ATAC | Translate_simple_RNA2ATAC |
TREE-class | An intermediate S4 class Tree that store tree info |
Vfilter_v3 | Function to filter variants, deprecated |
Vfilter_v4 | Function to filter variants, v4 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.