Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
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Documentation for package ‘immunarch’ version 0.9.1
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A B C D E F G H I J K L M N O P R S T V misc
-- A --
| AA_PROP | Tables with amino acid properties |
| aa_prop | Tables with amino acid properties |
| aa_properties | Tables with amino acid properties |
| AA_TABLE | Amino acid / codon table |
| aa_table | Amino acid / codon table |
| AA_TABLE_REVERSED | Amino acid / codon table |
| add_class | Add a new class attribute |
| add_pb | Set and update progress bars |
| apply_asymm | Apply function to each pair of data frames from a list. |
| apply_symm | Apply function to each pair of data frames from a list. |
| ATCHLEY | Tables with amino acid properties |
| atchley | Tables with amino acid properties |
-- B --
| bcrdata | BCR dataset |
| bunch_translate | Nucleotide to amino acid sequence translation |
-- C --
| chao1 | The main function for immune repertoire diversity estimation |
| check_distribution | Check and normalise distributions |
| clonal.prop | Clonality analysis of immune repertoires |
| clonality | Clonality analysis of immune repertoires |
| clonal_proportion | Clonality analysis of immune repertoires |
| clonal_space_homeostasis | Clonality analysis of immune repertoires |
| coding | Filter out coding and non-coding clonotype sequences |
| cross_entropy | Information measures |
-- D --
| dbAnnotate | Annotate clonotypes in immune repertoires using clonotype databases such as VDJDB and MCPAS |
| dbLoad | Load clonotype databases such as VDJDB and McPAS into the R workspace |
| diversity_eco | The main function for immune repertoire diversity estimation |
-- E --
| entropy | Information measures |
| exclude | Main function for data filtering |
-- F --
| fixVis | Manipulate ggplot plots and create publication-ready plots |
-- G --
| genes | Gene segments table |
| geneUsage | Main function for estimation of V-gene and J-gene statistics |
| geneUsageAnalysis | Post-analysis of V-gene and J-gene statistics: PCA, clustering, etc. |
| GENE_SEGMENTS | Gene segments table |
| gene_segments | Gene segments table |
| gene_stats | WIP |
| get.kmers | Calculate the k-mer statistics of immune repertoires |
| getKmers | Calculate the k-mer statistics of immune repertoires |
| get_aliases | Main function for estimation of V-gene and J-gene statistics |
| get_genes | Main function for estimation of V-gene and J-gene statistics |
| gini_coef | The main function for immune repertoire diversity estimation |
| gini_simpson | The main function for immune repertoire diversity estimation |
| group_from_metadata | Get a character vector of samples' groups from the input metadata file |
-- H --
| has_class | Check for the specific class |
| hill_numbers | The main function for immune repertoire diversity estimation |
-- I --
| immdata | Single chain immune repertoire dataset |
| immunarch_data_format | Specification of the data format used by immunarch dataframes |
| immunr_data_format | Specification of the data format used by immunarch dataframes |
| immunr_dbscan | Clustering of objects or distance matrices |
| immunr_hclust | Clustering of objects or distance matrices |
| immunr_kmeans | Clustering of objects or distance matrices |
| immunr_mds | Dimensionality reduction |
| immunr_pca | Dimensionality reduction |
| immunr_tsne | Dimensionality reduction |
| include | Main function for data filtering |
| inc_overlap | Incremental counting of repertoire similarity |
| inframes | Filter out coding and non-coding clonotype sequences |
| interval | Main function for data filtering |
| inverse_simpson | The main function for immune repertoire diversity estimation |
-- J --
| js_div | Information measures |
-- K --
| KIDERA | Tables with amino acid properties |
| kidera | Tables with amino acid properties |
| kl_div | Information measures |
| kmer_profile | Analysis immune repertoire kmer statistics: sequence profiles, etc. |
-- L --
| lessthan | Main function for data filtering |
-- M --
| makeKmerTable | Calculate the k-mer statistics of immune repertoires |
| matrixdiagcopy | Copy the upper matrix triangle to the lower one |
| morethan | Main function for data filtering |
-- N --
| noncoding | Filter out coding and non-coding clonotype sequences |
-- O --
| outofframes | Filter out coding and non-coding clonotype sequences |
-- P --
| process_col_argument | Return a column's name |
| properties | Tables with amino acid properties |
| publicRepertoire | Create a repertoire of public clonotypes |
| publicRepertoireApply | Apply transformations to public repertoires |
| publicRepertoireFilter | Filter out clonotypes from public repertoires |
| public_matrix | Get a matrix with public clonotype frequencies |
| pubRep | Create a repertoire of public clonotypes |
| pubRepApply | Apply transformations to public repertoires |
| pubRepFilter | Filter out clonotypes from public repertoires |
| pubRepStatistics | Statistics of number of public clonotypes for each possible combinations of repertoires |
-- R --
| rarefaction | The main function for immune repertoire diversity estimation |
| rare_proportion | Clonality analysis of immune repertoires |
| repAlignLineage | Aligns all sequences incliding germline within each clonal lineage within each cluster |
| repClonalFamily | Builds a phylogenetic tree using the sequences of a clonal lineage |
| repClonality | Clonality analysis of immune repertoires |
| repDiversity | The main function for immune repertoire diversity estimation |
| repExplore | Main function for exploratory data analysis: compute the distribution of lengths, clones, etc. |
| repFilter | Main function for data filtering |
| repGermline | Creates germlines for clonal lineages |
| repLoad | Load immune repertoire files into the R workspace |
| repOverlap | Main function for public clonotype statistics calculations |
| repOverlapAnalysis | Post-analysis of public clonotype statistics: PCA, clustering, etc. |
| repSample | Downsampling and resampling of immune repertoires |
| repSave | Save immune repertoires to the disk |
| repSomaticHypermutation | Calculates number of mutations against the germline for each clonotype |
-- S --
| scdata | Paired chain immune repertoire dataset |
| segments | Gene segments table |
| select_barcodes | Select specific clonotypes using barcodes from single-cell metadata |
| select_clusters | Split the immune repertoire data to clusters from single-cell barcodes |
| seqCluster | Function for assigning clusters based on sequences similarity |
| seqDist | Function for computing distance for sequences |
| set_pb | Set and update progress bars |
| spectratype | Immune repertoire spectratyping |
| split_to_kmers | Analysis immune repertoire kmer statistics: sequence profiles, etc. |
| switch_type | Return a column's name |
-- T --
| top | Get the N most abundant clonotypes |
| top_proportion | Clonality analysis of immune repertoires |
| trackClonotypes | Track clonotypes across time and data points |
| translate_bunch | Nucleotide to amino acid sequence translation |
-- V --
| vis | One function to visualise them all |
| vis.clonal_family | Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output |
| vis.clonal_family_tree | Visualise clonal family tree |
| vis.immunr_chao1 | Visualise diversity. |
| vis.immunr_clonal_prop | Visualise results of the clonality analysis |
| vis.immunr_dbscan | Visualisation of K-means and DBSCAN clustering |
| vis.immunr_div | Visualise diversity. |
| vis.immunr_dxx | Visualise diversity. |
| vis.immunr_dynamics | Visualise clonotype dynamics |
| vis.immunr_exp_clones | Visualise results of the exploratory analysis |
| vis.immunr_exp_count | Visualise results of the exploratory analysis |
| vis.immunr_exp_len | Visualise results of the exploratory analysis |
| vis.immunr_exp_vol | Visualise results of the exploratory analysis |
| vis.immunr_gene_usage | Histograms and boxplots (general case / gene usage) |
| vis.immunr_ginisimp | Visualise diversity. |
| vis.immunr_gu_matrix | Repertoire overlap and gene usage visualisations |
| vis.immunr_hclust | Visualisation of hierarchical clustering |
| vis.immunr_hill | Visualise diversity. |
| vis.immunr_homeo | Visualise results of the clonality analysis |
| vis.immunr_inc_overlap | Visualise incremental overlaps |
| vis.immunr_invsimp | Visualise diversity. |
| vis.immunr_kmeans | Visualisation of K-means and DBSCAN clustering |
| vis.immunr_kmer_table | Most frequent kmers visualisation. |
| vis.immunr_mds | PCA / MDS / tSNE visualisation (mainly overlap / gene usage) |
| vis.immunr_ov_matrix | Repertoire overlap and gene usage visualisations |
| vis.immunr_pca | PCA / MDS / tSNE visualisation (mainly overlap / gene usage) |
| vis.immunr_public_repertoire | Public repertoire visualisation |
| vis.immunr_public_statistics | Visualise sharing of clonotypes among samples |
| vis.immunr_rarefaction | Visualise diversity. |
| vis.immunr_tail_prop | Visualise results of the clonality analysis |
| vis.immunr_top_prop | Visualise results of the clonality analysis |
| vis.immunr_tsne | PCA / MDS / tSNE visualisation (mainly overlap / gene usage) |
| vis.step_failure_ignored | Handler for .nofail argument of pipeline steps that prevents examples from crashing on computers where certain dependencies are not installed |
| vis_bar | Bar plots |
| vis_box | Flexible box-plots for visualisation of distributions |
| vis_circos | Visualisation of matrices using circos plots |
| vis_heatmap | Visualisation of matrices and data frames using ggplo2-based heatmaps |
| vis_heatmap2 | Visualisation of matrices using pheatmap-based heatmaps |
| vis_hist | Visualisation of distributions using histograms |
| vis_immunr_kmer_profile_main | Visualise kmer profiles |
| vis_public_clonotypes | Visualisation of public clonotypes |
| vis_public_frequencies | Public repertoire visualisation |
| vis_seqlogo | Sequence logo plots for amino acid profiles. |
| vis_textlogo | Sequence logo plots for amino acid profiles. |
-- misc --
| .quant_column_choice | Get a column's name using the input alias |