| 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... |
| add_changes | add_changes |
| 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... |
| add_freq_raw | Convinient function that takes raw fragment, and out put... |
| AddHemSignature | Function to add hematopoietic signatures from... |
| add_hypermutable | add_hypermutable This function annotates the redeem@V.fitered... |
| add_raw_fragment | Produce a raw fragment table with frequency (how many cells)... |
| 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... |
| add_types | add_types |
| Annotate_base_change | Annotate_base_change |
| ATAC_Wrapper | Wrap Seurat ATAC clustering |
| BinaryDist | Compute distances for binary distances |
| binomialtest.msig.enrch_deplet | binomialtest.msig.enrch_deplet |
| clean_redeem | clean_redeem |
| clean_redeem_removehot | clean_redeem_removehotcall |
| 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 |
| convert_variant | convert_variant |
| CountOverlap_Adj | CountOverlap_Adj function to count the connectedness... |
| CountVperCell | Internal function in plot_variant |
| Create_mitoTracing | Create_mitoTracing |
| Create_redeemR | Create_redeemR |
| Create_redeemR_model | Create_redeemR_model |
| 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 |
| get_hype_v2 | get_hype_v2 This function annotates the redeem@V.fitered with... |
| 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_ks_test_df | Produce KS test results, input is the redeem object from... |
| 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_position_df_3.4 | Function needed to compute the |
| make_position_df_3.5 | make_position, but remain all the raw genotyp information... |
| 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 |
| redeemR.read.multiple.trim | Function to read in multiple runs of redeemV outputs with... |
| redeemR.read.trim | Function to read in redeemV outputs with edge trimming,... |
| 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,... |
| run_redeem_qc | run_redeem_qc |
| 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... |
| theme_cw1 | Define a custom theme function |
| theme_cw2 | Define a custom theme function |
| 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 |
