AbForests_AntibodyForest | Infer and draw B cell evolutionary networks |
AbForests_CompareForests | Comparison of distinct B cell repertoires |
AbForests_ConvertStructure | Extract transcriptome/isotype information and B cell receptor sequences from single cell immune repertoire formatted as list of data.frames |
AbForests_CsvToDf | Convert list of csvs, to nested list of data.frames |
AbForests_ForestMetrics | Calculate metrics for networks |
AbForests_PlotGraphs | Plot igraph and ggplot objects |
AbForests_PlyloToMatrix | Conversion of phylogenetic tree to distance matrix |
AbForests_RemoveNets | Filter sub-repertoires with less than N unique sequences or with less than C unique cells |
AbForests_SubRepertoiresByCells | Split single cell immune repertoire into sub-repertoires by isotype based on number of B cells |
AbForests_SubRepertoiresByUniqueSeq | Split single cell immune repertoire into sub-repertoires by isotype based on number of unique sequences |
AbForests_UniqueAntibodyVariants | Count the number of unique antibody variants per clonal lineage |
automate_GEX | GEX processing wrapper in Platypus V2 |
Bcell_sequences_example_tree | Example csv file 1 |
Bcell_tree_2 | Example csv file 2 |
call_MIXCR | Calls MiXCR VDJ object of Platypus V2 |
class_switch_prob_hum | class_switch_prob_hum The probability matrix of class switching for human b cells. The row names of the matrix are the isotypes the cell is switching from, the column names are the isotypes the cell is switching to. All B cells start from IGHM, and switch to one of the other isotypes or remain the same. |
class_switch_prob_mus | class_switch_prob_mus The probability matrix of class switching for mouse b cells. The row names of the matrix are the isotypes the cell is switching from, the column names are the isotypes the cell is switching to. All B cells start from IGHM, and switch to one of the other isotypes or remain the same. |
clonofreq | Plot clonal frequency barplot of the outout simulated data |
clonofreq.isotype.data | Get information about the clonotype counts grouped by isotype. |
clonofreq.isotype.plot | Get information about the clonotype counts grouped by isotype. |
clonofreq.trans.data | Get information about the clonotype counts grouped by transcriptome state(cell type). |
clonofreq.trans.plot | Get information about the clonotype counts grouped by transcriptome state(cell type). |
cluster.id.igraph | Get clone network igraphs colored by seurat cluster id. |
colors | colors A vector of characters specifying colors used in igraph phylogenetic tree. Default colors: "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3" ,"#A6D854" |
Echidna_simulate_repertoire | Simulate immune repertoire and transcriptome data |
Echidna_vae_generate | Simulate B or T cell receptor sequences by variational autoencodes(VAEs) trained with experimental data. |
get.avr.mut.data | Get information about somatic hypermutation in the simulation. This function return a barplot showing the average mutation. |
get.avr.mut.plot | Get information about somatic hypermutation in the simulation. This function return a barplot showing the average mutation. |
get.barplot.errorbar | Return a barplot of mean and standard error bar of certain value of each clone. |
get.elbow | Get the seurat object from simulated transciptome output. |
get.n.node.data | Get the number of unique variants in each clone in a vector. The output is the vector representing the numbers of unique variants. |
get.n.node.plot | Get the number of unique variants in each clone in a vector and the barplot. The first item in the output is the vector representing the numbers of unique variants, the second item is the barplot. |
get.seq.distance | Computing sequence distance according to the number of unmatched bases. |
get.umap | Further process the seurat object from simulated transciptome output and make UMAP ready for plotting. |
get.vgu.matrix | Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p<-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function. |
GEX_clonotype | Platypus V2 GEX and VDJ integration for clonotypes |
GEX_cluster_genes | Differentially expressed genes between clusters or data subsets |
GEX_cluster_genes_heatmap | Heatmap of cluster defining genes |
GEX_cluster_membership | Cluster membership plots by sample |
GEX_coexpression_coefficient | Coexpression of selected genes |
GEX_DEgenes | Wrapper for differential gene expression analysis and plotting |
GEX_DEgenes_persample | Platypus V2 Differentially expressed genes |
GEX_dottile_plot | GEX Dottile plots |
GEX_GOterm | GEX GO-Term analysis and plotting |
GEX_GSEA | GEX Gene Set Enrichment Analysis and plotting |
GEX_heatmap | Flexible GEX heatmap wrapper |
GEX_pairwise_DEGs | Wrapper for calculating pairwise differentially expressed genes |
GEX_phenotype | Assignment of cells to phenotypes based on selected markers |
GEX_phenotype_per_clone | Plotting of GEX phenotype by VDJ clone |
GEX_proportions_barplot | Plots proportions of a group of cells within a secondary group of cells. E.g. The proportions of samples in seurat clusters, or the proportions of samples in defined cell subtypes |
GEX_scatter_coexpression | Scatter plot for coexpression of two selected genes |
GEX_topN_DE_genes_per_cluster | Platypus V2 GEX DE genes helper |
GEX_visualize_clones | Platypus V2 GEX and VDJ integration for visualizing clone clustering |
GEX_volcano | Flexible wrapper for GEX volcano plots |
hotspot_df | hotspot_df Hotspot mutations taken from Yaari et al., Frontiers in Immunology, 2013. This contains transition probabilities for all 5mer combinations based on high throughput sequencing data. The transition probabilities are for the middle nucleotide in each 5mer set. This can be customized by changing the genes and sequences. Custom mutation hotspots can be supplied by modifying this dataframe. Repeating particular hotspot entries allows for the hotspot to mutate more than one time per SHM event. |
hum_b_h | hum_b_h |
hum_b_l | hum_b_l |
hum_t_h | hum_t_h |
hum_t_l | hum_t_l |
iso_SHM_prob | iso_SHM_prob A probability dataframe specifying SHM.nuc.prob for cells of different isotypes. The first column is the names of isotypes, while the second column is the SHM.nuc.prob of cell of that isotype. user can define different SHM.nuc.prob for isotypes. |
mus_b_h | mus_b_h |
mus_b_l | mus_b_l |
mus_b_trans | mus_b_trans A data frame contains mouse B cell average gene expression for multiple cell types, with the rows representing the gene names, column names representing the cell type names. The original single cell sequencing data is retrieved from 10xgenomics and combined with experimental data from.#? The expression level for different cell types are obtained by calculating the average expression after sorting the original data by markers as shown below. NaiveBcell Cd19+;Cd27-;Cd38- GerminalcenterBcell Fas+;Cd19+ Plasmacell Sdc1+ MemoryBcell Cd38+;Fas- |
mus_t_h | mus_t_h |
mus_t_l | mus_t_l |
no.empty.node | Get clone network igraphs without empty mode. Empty node represents the 'extincted' sequences, that are not in any living cell but once existed. |
one_spot_df | one_spot_df |
pheno_SHM_prob | pheno_SHM_prob A probability dataframe specifying SHM.nuc.prob for cells of different phenotypes. The first column is the names of phenotypes, while the second column is the SHM.nuc.prob of cell of that phenotype. user can define different SHM.nuc.prob for phenotypes. |
PlatypusDB_AIRR_to_VGM | AIRR to Platypus V3 VGM compatibility function |
PlatypusDB_fetch | Loads and saves RData objects from the PlatypusDB |
PlatypusDB_find_CDR3s | CDR3 query function for PlatypusDB |
PlatypusDB_list_projects | Metadata download by project for PlatypusDB |
PlatypusDB_load_from_disk | PlatypusDB utility for import of local datasets |
PlatypusDB_VGM_to_AIRR | Platypus V3 VGM to AIRR compatibility function |
select.top.clone | Get the index of top ranking clones. |
small_vgm | Small VDJ GEX matrix (VGM) for function testing purposes |
special_v | special_v a dataframe, of heavy and light chain v gene combination and their probability to be selected for expansion. |
trans_switch_prob_b | trans_switch_prob_b The probability for B cell transcriptome states switching. The row names of the matrix are the cell states the cell is switching from, the column names are the cells states the cell is switching to. |
trans_switch_prob_t | trans_switch_prob_t The probability for T cell transcriptome states switching. The row names of the matrix are the cell states the cell is switching from, the column names are the cells states the cell is switching to. |
umap.top.highlight | Set idents for top abundant clones in Seurat object, get ready for highlight the top abundant clones in UMAP. |
VDJ_abundances | Calculate abundances/counts of specific features for a VDJ dataframe |
VDJ_alpha_beta_Vgene_circos | Circos plot for VDJ and VJ pairings |
VDJ_analyze | Platypus V2 VDJ processing wrapper. |
VDJ_antigen_integrate | Integrates antigen-specific information into the VDJ/VDJ.GEX.matrix[[1]] object |
VDJ_assemble_for_PnP | Ab sequence assembly for recombinant PnP expression |
VDJ_bulk_to_vgm | Utility function for bulk data to standard Platypus format conversion |
VDJ_call_MIXCR | MiXCR wrapper for Platypus V3 VDJ object |
VDJ_call_recon | Calls the Kaplinsky/RECON tool |
VDJ_circos | Internal utility for circos functions |
VDJ_clonal_donut | Circular VDJ expansion plots |
VDJ_clonal_expansion | Flexible wrapper for clonal expansion barplots by isotype, GEX cluster etc. |
VDJ_clonal_expansion_abundances | Wrapper function for VDJ_abundances to obtain ranked clonotype barplots |
VDJ_clonal_lineages | Platypus V2 lineage utility |
VDJ_clonotype | Deprecated Platypus V2 clonotyping wrapper |
VDJ_clonotype_clusters_circos | Circos plot for clonotype - GEX cluster pairings |
VDJ_clonotype_v3 | Platypus V3 clonotyping wrapper |
VDJ_contigs_to_vgm | Local VDJ dataframe to VDJ.GEX.matrix format utility |
VDJ_db_annotate | Wrapper function of VDJ_antigen_integrate function |
VDJ_db_load | Load and preprocess a list of antigen-specific databases |
VDJ_diversity | Diversity metrics for VDJ |
VDJ_dublets | Platypus V2 annotation utility |
VDJ_dynamics | Tracks a specific VDJ column across multiple samples/timepoints. |
VDJ_expand_aberrants | Expand the aberrant cells in a VDJ dataframe by converting them into additional rows |
VDJ_extract_germline | Platypus V2 utility for full germline sequence via MiXCR |
VDJ_get_public | Function to get shared/public elements across multiple repertoires |
VDJ_GEX_clonal_lineage_clusters | Platypus V2 lineage - GEX integration utility |
VDJ_GEX_expansion | Platypus V2 utility |
VDJ_GEX_integrate | only Platypus v2 Integrates VDJ and gene expression libraries by providing cluster membership seq_per_vdj object and the index of the cell in the Seurat RNA-seq object. |
VDJ_GEX_matrix | VDJ GEX processing and integration wrapper |
VDJ_GEX_overlay_clones | Overlay clones on GEX projection |
VDJ_GEX_stats | Standalone VDJ and GEX statistics. |
VDJ_isotypes_per_clone | Platypus V2 clonal utility |
vdj_length_prob | vdj_length_prob A list dataframe specifying lengths and probabilities of bases deleted or inserted at each junction site of VDJ recombination event. v3_deletion length and probability of deleted bases at 3' end of V segment d5_deletion length and probability of deleted bases at 5' end of D segment d3_deletion length and probability of deleted bases at 3' end of D segment j5_deletion length and probability of deleted bases at 5' end of J segment dj_insertion length and probability of inserted bases between D-J segment vj_insertion length and probability of inserted bases between V-J segment for light or alpha chains |
VDJ_logoplot_vector | Flexible logoplot wrapper |
VDJ_network | Similarity networks based on CDR3 regions |
VDJ_overlap_heatmap | Wrapper to determine and plot overlap between VDJ features across groups |
VDJ_per_clone | VDJ_per_clone |
VDJ_phylogenetic_trees | Creates phylogenetic trees from a VDJ dataframe |
VDJ_phylogenetic_trees_plot | Phylogenetic tree plotting |
VDJ_plot_SHM | Plotting of somatic hypermutation counts |
VDJ_reclonotype_list_arrange | Platypus V2 dataframe utility |
VDJ_tree | Platypus V2 phylogenetic trees. |
VDJ_variants_per_clone | Wrapper for variant analysis by clone |
VDJ_Vgene_usage | V(D)J gene usage stacked barplots |
VDJ_Vgene_usage_barplot | V(D)J gene usage barplots |
VDJ_Vgene_usage_stacked_barplot | V(D)J gene usage stacked barplots |
VDJ_VJ_usage_circos | Makes a Circos plot from the VDJ_analyze output. Connects the V gene with the corresponding J gene for each clonotype. |
VGM_expanded_clones | VDJ utility for T/F column for clonal expansion |
VGM_expand_featurebarcodes | Utility for feature barcode assignment including clonal information |
VGM_integrate | Utility for VDJ GEX matrix to integrated VDJ and GEX objects after addition of data to either |