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
AlphaFold_prediction    Structure prediction of Mixcr wrapper output
                        with Alpha Fold
AntibodyForests         Infer B cell evolutionary networks and/or
                        sequence similarity networks
AntibodyForests_communities
                        Network clustering/community detection for the
                        AntibodyForests similarity networks
AntibodyForests_dynamics
                        Create a nested list of longitudinal
                        AntibodyForests objects
AntibodyForests_embeddings
                        Structural node embeddings for the
                        AntibodyForests minimum spanning trees/
                        sequence similarity networks
AntibodyForests_expand_intermediates
                        Infer intermediate nodes in the minimum
                        spanning trees/ sequences similiarity networks
                        created by the AntibodyForests function
AntibodyForests_heterogeneous
                        Bipartite sequence-cell networks in
                        AntibodyForests
AntibodyForests_infer_ancestral
                        Creates phylogenetic trees, infers ancestral
                        sequences, and converts the resulting trees
                        into igraph objects.
AntibodyForests_join_trees
                        Joins a list of trees/networks as
                        AntibodyForests objects into a single
                        AntibodyForests object
AntibodyForests_kernels
                        Graph kernel methods for graph
                        structure/topology comparisons
AntibodyForests_label_propagation
                        Propagate label annotations/values on sparsely
                        labeled networks as AntibodyForests objects.
AntibodyForests_metrics
                        Node metrics for the AntibodyForests sequence
                        similarity networks and minimum spanning trees.
AntibodyForests_node_transitions
                        Calculates the node transitions frequencies for
                        a given feature and an AntibodyForests object
AntibodyForests_overlap
                        Edge overlap heatmaps for a set of
                        AntibodyForests sequence similarity networks or
                        minimum spanning trees.
AntibodyForests_paths   Calculates the longest/shortest paths from a
                        node to a given node for the AntibodyForests
                        minimum spanning trees / sequence similarity
                        networks
AntibodyForests_phylo   Converts the igraph networks of a given
                        AntibodyForests object into a given (useful to
                        convert the minimum spanning trees into a
                        phylogenetic tree)
AntibodyForests_plot    Custom plots for trees/networks created with
                        AntibodyForests
AntibodyForests_plot_metrics
                        Plots the resulting node metrics from the
                        AntibodyForests_metrics function
Bcell_sequences_example_tree
                        Example csv file 1
Bcell_tree_2            Example csv file 2
CellPhoneDB_analyse     Cellphone DB utility
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.
GEX_DEgenes             Wrapper for differential gene expression
                        analysis and plotting
GEX_DEgenes_persample   Platypus V2 Differentially expressed genes
GEX_GOterm              GEX GO-Term analysis and plotting
GEX_GSEA                GEX Gene Set Enrichment Analysis and plotting
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_dottile_plot        GEX Dottile plots
GEX_gene_visualization
                        Visualization of marker expression in a data
                        set or of predefined genes (B cells, CD4 T
                        cells and CD8 T cells).
GEX_heatmap             Flexible GEX heatmap wrapper
GEX_lineage_trajectories
                        This is a function to infer single cell
                        trajectories and identifying lineage structures
                        on clustered cells. Using the slingshot library
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_projecTILS          ProjectTILs tool utility
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_pseudobulk          Function that performs pseudo-bulking on the
                        data (VGM input), according to criteria
                        specified by the User, and uses the
                        pseudo-bulked data to perform Differential Gene
                        Expression (DGE) analysis.
GEX_pseudotime_trajectory_plot
                        This function plots pseudotime along the
                        trajectories which have been constructed with
                        the GEX_trajectories() function.
GEX_scatter_coexpression
                        Scatter plot for coexpression of two selected
                        genes
GEX_topN_DE_genes_per_cluster
                        Platypus V2 GEX DE genes helper
GEX_trajectories        This is a function which infers trajectories
                        along ordered cells on dimensionality reduced
                        data. It projects trajectrories on a dim. red.
                        plot such as Umap. This uses Monocle3 or
                        Monocle2.
GEX_visualize_clones    Platypus V2 GEX and VDJ integration for
                        visualizing clone clustering
GEX_volcano             Flexible wrapper for GEX volcano plots
PlatypusDB_AIRR_to_VGM
                        AIRR to Platypus V3 VGM compatibility function
PlatypusDB_VGM_to_AIRR
                        Platypus V3 VGM to AIRR 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
PlatypusML_balance      Secondary ML for crossvalidation
PlatypusML_classification
                        Core ML for crossvalidation
PlatypusML_feature_extraction_GEX
                        Extraction of features from GEX matrix of VGM
PlatypusML_feature_extraction_VDJ
                        Extraction of features from VDJ table of VGM
Spatial_VDJ_assignment
                        Assign simulated immune repertoire sequences
                        (BCR or TCR) simulated by Echidna to
                        transcriptome and location in a spatial image
                        in function of cell type.
Spatial_VDJ_plot        Plotting immune repertoire data as clonotype or
                        isotype for cells on a spatial image.
Spatial_celltype_plot   Plotting celltype assign to cell according to
                        their phenotype on the spatial image.
Spatial_cluster         Plotting clusters of cells by choosing between
                        10X Genomics clustering or reclustering the
                        cells.
Spatial_density_plot    Plotting the contour density of selected cells
                        or of all cells.
Spatial_evolution_of_clonotype_plot
                        Plotting the phylogenetic network of a
                        clonotype based on the somatic hypermutations
                        of the immune repertoire sequences on a spatial
                        image.
Spatial_marker_expression
                        Plotting a gene of interest in selected cells
                        on the spatial image.
Spatial_module_expression
                        Plotting the expression of a gene module on the
                        spatial image with or without a threshold.
Spatial_nb_SHM_compare_to_germline_plot
                        Plotting number of somatic hypermutation of
                        clones compare to the germline sequence of the
                        clonotype.
Spatial_scaling_parameters
                        Scaling of the spatial parameters to be able to
                        express the gene expression on the spatial
                        image.
Spatial_selection_expanded_clonotypes
                        Selection of VGM[[1]]/VDJ data of the x more
                        expanded clonotypes.
Spatial_selection_of_cells_on_image
                        Allows to select an area on the spatial image
                        and to isolate the cells expressed on this part
                        and repeat this process several times.
Spatial_vgm_formation   Addition of the spatial information to the VGM
                        matrix, output of VDJ_GEX_matrix()
VDJ_GEX_clonal_lineage_clusters
                        Platypus V2 lineage - GEX integration utility
VDJ_GEX_clonotyme       Pseudotime analysis for scRNA and repertoire
                        sequencing datasets
VDJ_GEX_clonotype_clusters_circos
                        Makes a Circos plot from the VDJ_GEX_integrate
                        output. Connects the clonotypes with the
                        corresponding clusters.
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_VJ_usage_circos     Makes a Circos plot from the VDJ_analyze
                        output. Connects the V gene with the
                        corresponding J gene for each clonotype.
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_abundances          Calculate abundances/counts of specific
                        features for a VDJ dataframe
VDJ_alpha_beta_Vgene_circos
                        Produces a Circos plot from the VDJ_analyze
                        output. Connects the V-alpha with the
                        corresponding V-beta gene for each clonotype.
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_MIXCR_full     MiXCR wrapper for Platypus V3 VDJ object. In
                        addition to the VDJ_call_MIXCR function, the
                        output also contains the concatenated sequences
                        from FR1 all the way to FR2 for both the VDJ
                        and VJ.
VDJ_call_RECON          Calls the Kaplinsky/RECON tool
VDJ_call_enclone        (Re)clonotype a VDJ object using cellranger's
                        enclone tool
VDJ_circos              Plots a Circos diagram from an adjacency
                        matrix. Uses the Circlize chordDiagram
                        function. Is called by
                        VDJ_clonotype_clusters_circos(),
                        VDJ_alpha_beta_Vgene_circos() and
                        VDJ_VJ_usage_circos() functions or works on its
                        own when supplied with an adjacency matrix.
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           Platypus V3 clonotyping wrapper
VDJ_contigs_to_vgm      Formats "VDJ_contigs_annotations.csv" files
                        from cell ranger to match the VDJ_GEX_matrix
                        output using only cells with 1VDJ and 1VJ chain
VDJ_db_annotate         Wrapper function of VDJ_antigen_integrate
                        function
VDJ_db_load             Load and preprocess a list of antigen-specific
                        databases
VDJ_diversity           Calculates and plots common diversity and
                        overlap measures for repertoires and alike.
                        Requires the vegan package
VDJ_dublets             Platypus V2 annotation utility
VDJ_dynamics            Tracks a specific VDJ column across multiple
                        samples/timepoints.
VDJ_enclone             Updated clonotyping function based on
                        implications for cells with different chain
                        numbers than 1 VDJ 1 VJ chains.
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_isotypes_per_clone
                        Platypus V2 clonal utility
VDJ_kmers               Calculates and plots kmers distributions and
                        frequencies.
VDJ_logoplot_vector     Flexible logoplot wrapper
VDJ_network             Similarity networks based on CDR3 regions
VDJ_ordination          Performs ordination/dimensionality reduction
                        for a species incidence matrix, depending on
                        the species selected in the feature.columns
                        parameter.
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_public              Function to get shared/public elements across
                        multiple repertoires
VDJ_rarefaction         Plots rarefaction curves for species denoted in
                        the feature.columns parameter across groups
                        determined by grouping.columns
VDJ_reclonotype_list_arrange
                        Platypus V2 dataframe utility
VDJ_select_clonotypes   Select clonotypes
VDJ_structure_analysis
                        Analysis of antibody structures
VDJ_tree                Platypus V2 phylogenetic trees.
VDJ_variants_per_clone
                        Wrapper for variant analysis by clone
VGM_expand_featurebarcodes
                        Utility for feature barcode assignment
                        including clonal information
VGM_expanded_clones     VDJ utility for T/F column for clonal expansion
VGM_integrate           Utility for VDJ GEX matrix to integrated VDJ
                        and GEX objects after addition of data to
                        either
automate_GEX            GEX processing wrapper in Platypus V2
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"
dot_plot                Function to cutomise the Dot Plot of
                        CellPhoneDB analysis results.
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.
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 The expression level for
                        different cell types are obtained by
                        calculating the average expression after
                        sorting the original data by markers as shown
                        below.
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.
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_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.
