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
Bcell_sequences_example_tree
                        Example csv file 1
Bcell_tree_2            Example csv file 2
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             Extracts the differentially expressed genes
                        between two groups of cells. These groups are
                        defined as cells having either of two entries
                        (group1, group2) in the grouping.column of the
                        input Seurat object metadata This function uses
                        the FindMarkers function from the Seurat
                        package.
GEX_DEgenes_persample   !Only for Platypus version v2. For more
                        flexibility and platypus v3 please refer to
                        GEX_Degenes. Extracts the differentially
                        expressed genes between two samples. This
                        function uses the FindMarkers function from the
                        Seurat package. Further parameter control can
                        be accomplished by calling the function
                        directly on the output of automate_GEX and
                        further extracting sample information from the
                        "sample_id" component of the Seurat object.
GEX_GOterm              Runs a GO term analysis on a submitted list of
                        genes. Works with the output of
                        GEX_topN_DE_genes_per_cluster or a custom list
                        of genes to obtain GOterms.
GEX_GSEA                Conducts a Gene Set Enrichment Analysis (GSEA)
                        on a set of genes submitted in a data frame
                        with a metric each. Works with the output of
                        GEX_genes_cluster or a custom data frame
                        containing the gene symbols either in a column
                        "symbols" or as rownames and a metric for each
                        gene. The name of the column containing the
                        metric has to be declared via the input
                        metric.colname.
GEX_automate            Automates the transcriptional analysis of the
                        gene expression libraries from cellranger. This
                        function will integrate multiple samples
GEX_clonotype           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.
GEX_cluster_genes       Extracts the differentially expressed genes
                        between two samples. This function uses the
                        FindMarkers function from the Seurat package.
                        Further parameter control can be accomplished
                        by calling the function directly on the output
                        of automate_GEX or VDJ_GEX_matrix
GEX_cluster_genes_heatmap
                        Produces a heatmap displaying the expression of
                        the top genes that define each cluster in the
                        Seurat object. The output heatmap is derived
                        from DoHeatmap from Seurat and thereby can be
                        edited using typical ggplot interactions. The
                        number of genes per cluster and the nunber of
                        cells to display can be specified by the user.
                        Either the log fold change or the p value can
                        be used to select the top n genes.
GEX_cluster_membership
                        Plots the cluster membership for each of the
                        distinct samples in the Seurat object from the
                        automate_GEX function. The distinct samples are
                        determined by "sample_id" field in the Seurat
                        object.
GEX_coexpression_coefficient
                        Returns eiter a plot or numeric data of
                        coexpression levels of selected
                        genes.Coexpression % is calculated as the
                        quotient of double positive cells (counts \> 0)
                        and the sum of total cells positive for either
                        genes.
GEX_dottile_plot        Outputs a dotplot for gene expression, where
                        the color of each dot is scaled by the gene
                        expression level and the size is scaled by the
                        % of cells positive for the gene
GEX_heatmap             Produces a heatmap containing gene expression
                        information at the clonotype level. The rows
                        correspond to different genes that can either
                        be determined by pre-made sets of B or T cell
                        markers, or can be customized by the user. The
                        columns correspond to individual cells and the
                        colors correspond to the different clonotype
                        families.
GEX_pairwise_DEGs       Produces and saves a list of volcano plots with
                        each showing differentially expressed genes
                        between pairs groups. If e.g. seurat_clusters
                        used as group.by, a plot will be generated for
                        every pairwise comparison of clusters. For
                        large numbers of this may take longer to run.
                        Only available for platypus v3
GEX_phenotype           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.
GEX_phenotype_per_clone
                        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. ! For platypus.version == "v3" and
                        VDJ_GEX_matrix output the function will iterate
                        over entries in the sample_id column of the GEX
                        by default.
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
                        Clonal frequency plot displaying clonal
                        expansion for either T and B cells with
                        Platypus v3 input.
GEX_topN_DE_genes_per_cluster
                        Organizes the top N genes that define each
                        Seurat cluster and converts them into a single
                        dataframe. This can be useful for obtaining
                        insight into cluster-specific phenotypes.
GEX_visualize_clones    !Only for platypus version v2. For platypus v3
                        refer to: VDJ_GEX_overlay_clones() Visualize
                        selected clonotypes on the tSNE or UMAP
                        projection.
GEX_volcano             Plots a volcano plot from the output of the
                        FindMarkers function from the Seurat package or
                        the GEX_cluster_genes function alternatively.
PlatypusDB_AIRR_to_VGM
                        Loads in and converts input AIRR-compatible tsv
                        file(s) into the Platypus VGM object format.
PlatypusDB_VGM_to_AIRR
                        Exports AIRR compatible tables supplemented
                        with VDJ and GEX information from the Platypus
                        VGM object and the cellranger output
                        airr_rearrangements.tsv
PlatypusDB_fetch        Loads and saves RData objects from the
                        PlatypusDB
PlatypusDB_find_CDR3s   Queries for the occurrence of CDR3 sequences in
                        public datasets on PlatypusDB.
PlatypusDB_list_projects
                        Lists metadata tables of available projects on
                        PlatypusDB
PlatypusDB_load_from_disk
                        Utility function for loading in local dataset
                        as VDJ_GEX_matrix and PlatypusDB compatible R
                        objects. Especially useful when wanting to
                        integrate local and public datasets. This
                        function only imports and does not make changes
                        to format, row and column names. Exception:
                        filtered_contig.fasta are appended to the
                        filtered_contig_annotations.csv as a column for
                        easy access
VDJ_GEX_clonal_lineage_clusters
                        only Platypus v2 Integrates the transcriptional
                        cluster information into the clonal lineages.
                        This requires that automate_GEX,
                        VDJ_clonal_lineages, and VDJ_GEX_integrate have
                        already been ran. The transcriptional cluster
                        will be added to the end of the Name for each
                        sequence.
VDJ_GEX_expansion       only Platypus v2 Integrates VDJ and gene
                        expression libraries by providing cluster
                        membership seq_per_vdj object. Output will plot
                        which transcriptional cluster (GEX) that the
                        cells of a given clonotype are found in.
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          Processes both raw VDJ and GEX Cellranger
                        output to compile a single cell level table
                        containing all available information for each
                        cell. If using Feature Barcodes please note the
                        [FB] paragraph in the description and all "FB."
                        parameters
VDJ_GEX_overlay_clones
                        Highlights the cells belonging to any number of
                        top clonotypes or of specifically selected
                        clonotypes from one or more samples or groups
                        in a GEX dimensional reduction.
VDJ_GEX_stats           Gives stats on number and quality of reads.
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         Produces a matrix counting the number of
                        occurences for each VDJ and VJ Vgene
                        combinations for each list enty in
                        VDJ.clonotype.output or for each sample_id in
                        VDJ.matrix
VDJ_Vgene_usage_barplot
                        Produces a barplot with the most frequently
                        used IgH and IgK/L Vgenes.
VDJ_Vgene_usage_stacked_barplot
                        Produces a stacked barplot with the fraction of
                        the most frequently used IgH and IgK/L Vgenes.
                        This function can be used in combination with
                        the VDJ_Vgene_usage_barplot to vizualize V gene
                        usage per sample and among samples.
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 Processes and organizes the
                        repertoire sequening data from cellranger vdj
                        and returns a list of dataframes, where each
                        dataframe corresponds to an individual
                        repertoire. The function will return split CDR3
                        sequences, germline gene information, filter
                        out those clones with either incomplete
                        information or doublets (multiple CDR3
                        sequences for a given chain). This function
                        should be called once for desired integrated
                        repertoire and transcriptome. For example, if
                        there are 3 VDJ libraries and 3 GEX libraries
                        and the goal is to analyze all three GEX
                        libraries together (e.g. one UMAP/tSNE
                        reduction) this then function should be called
                        one time and the three VDJ directories should
                        be provided as input to the single function
                        call.
VDJ_antigen_integrate   Integrates antigen-specific information into
                        the VDJ/VDJ.GEX.matrix[[1]] object
VDJ_assemble_for_PnP    Assembles sequences from MIXCR output into
                        inserts for expression in PnP cells. For
                        detailes check
                        https://doi.org/10.1038/ncomms12535 ! ALWAYS
                        VALIDATE INDIVIDUAL SEQUENCE IN GENEIOUS OR
                        OTHER SOFTWARE BEFORE ORDERING SEQUENCES FOR
                        EXPRESSION ! Check notes on column content
                        below ! Only cells with 1 VDJ and 1 VJ sequence
                        are considered. Warnings are issued if
                        sequences do not pass necessary checks
VDJ_call_MIXCR          Extracts information on the VDJRegion level
                        using MiXCR on WINDOWS, MAC and UNIX systems
                        for input from both Platypus v2 (VDJ.per.clone)
                        or v3 (Output of VDJ_GEX_matrix) This function
                        assumes the user can run an executable instance
                        of MiXCR and is elgible to use MiXCR as
                        determined by license agreements. ! FOR WINDOWS
                        USERS THE EXECUTABLE MIXCR.JAR HAS TO PRESENT
                        IN THE CURRENT WORKING DIRECTORY ! The
                        VDJRegion corresponds to the recombined heavy
                        and light chain loci starting from framework
                        region 1 (FR1) and extending to frame work
                        region 4 (FR4). This can be useful for
                        extracting full-length sequences ready to clone
                        and further calculating somatic hypermutation
                        occurrences.
VDJ_call_recon          Calls the Kaplinsky/RECON 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        Generate circular plots of clonal expansion per
                        repertoire directly from the VDJ matrix of the
                        VDJ_GEX_matrix function
VDJ_clonal_expansion    Clonal frequency plot displaying clonal
                        expansion for either T and B cells with
                        Platypus v3 input. Only available for Platypus
                        "v3" available. For v2 plotting of B cell
                        clonotype expansion and isotypes please refer
                        to VDJ_isotypes_per_clone.
VDJ_clonal_expansion_abundances
                        Wrapper function for VDJ_abundances to obtain
                        ranked clonotype barplots
VDJ_clonal_lineages     Only Platypus V2 Organizes and extracts
                        full-length sequences for clonal lineage
                        inference. The output sequence can either
                        contain the germline sequence as determined by
                        cellranger or can just contain the sequences
                        contained in each clonal family.
VDJ_clonotype           Deprecated function for Platypus V2 with
                        options for Platypus V3. For revised
                        hierarchical clonotyping please use
                        VDJ_clonotype_v3() Returns a list of clonotype
                        dataframes following additional clonotyping.
                        This function works best following filtering to
                        ensure that each clone only has one heavy chain
                        and one light chain.
VDJ_clonotype_clusters_circos
                        Makes a Circos plot from the VDJ_GEX_integrate
                        output. Connects the clonotypes with the
                        corresponding clusters.
VDJ_clonotype_v3        Updated clonotyping function based on
                        implications for cells with different chain
                        numbers than 1 VDJ 1 VJ chains.
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.
                        Require the vegan package
VDJ_dublets             Only Platypus v2 Produces a matrix indicating
                        either the number of cells or clones which
                        contain multiple heavy or light chains (or
                        alpha/beta in the case of T cells).
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    Only Platypus v2 Extracts the full-length
                        germline sequence as determined by cellranger.
                        This function returns an object that now
                        contains the reference germline for each of the
                        clones. If multiple clones (as determined by
                        cellranger) have been merged using the
                        VDJ_clonotype function then these sequences may
                        have distinct germline sequences despite being
                        in the same clonal family (nested list). This
                        is particularly possible when homology
                        thresholds were used to determine the
                        clonotypes.
VDJ_get_public          Function to get shared/public elements across
                        multiple repertoires
VDJ_isotypes_per_clone
                        Only for Platypus v2 Clonal frequency plot
                        displaying the isotype usage of each clone. !
                        For platypus v3 use VDJ_clonal_expansion
VDJ_logoplot_vector     Plots a logoplot of the CDR3 aminoacid region
VDJ_network             Creates a similarity network where clones with
                        similar CDR3s are connected.
VDJ_overlap_heatmap     Yields overlap heatmap and datatable of
                        features or combined features for different
                        samples or groups
VDJ_per_clone           VDJ_per_clone
VDJ_phylogenetic_trees
                        Creates phylogenetic trees from a VDJ dataframe
VDJ_phylogenetic_trees_plot
                        Function to plot phylogenetic trees obtained
                        from VDJ_phylogenetic_trees
VDJ_plot_SHM            Plots for SHM based on MIXCR output generated
                        using the VDJ_call_MIXCR function and appended
                        to the VDJ.GEX.matrix.output
VDJ_reclonotype_list_arrange
                        Only Platypus v2 Organizes the top N genes that
                        define each Seurat cluster and converts them
                        into a single dataframe. This can be useful for
                        obtaining insight into cluster-specific
                        phenotypes.
VDJ_tree                only Platypus v2 Produces neighbor joining
                        phylogenetic trees from the output of
                        VDJ_clonal_lineages
VDJ_variants_per_clone
                        Returns statistics and plots to examine
                        diversity of any sequence or metadata item
                        within clones on a by sample level or global
                        level
VGM_expand_featurebarcodes
                        Replaces the original sample_id column of a vgm
                        object with a pasted version of the original
                        sample_id and the last digits of the feature
                        barcode.
automate_GEX            Automates the transcriptional analysis of the
                        gene expression libraries from cellranger. This
                        function will integrate multiple samples
call_MIXCR              Extracts information on the VDJRegion level
                        using MiXCR. This function assumes the user can
                        run an executable instance of MiXCR and is
                        elgible to use MiXCR as determined by license
                        agreements. The VDJRegion corresponds to the
                        recombined heavy and light chain loci starting
                        from framework region 1 (FR1) and extending to
                        frame work region 4 (FR4). This can be useful
                        for extracting full-length sequences ready to
                        clone and further calculating somatic
                        hypermutation occurances.
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"
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 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.
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. 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
