Man pages for charlotterich/immunarch_code
Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires in R
| aa_properties | Tables with amino acid properties |
| aa_table | Amino acid / codon table |
| add_class | Add a new class attribute to the input object. |
| apply_symm | Apply function to each pair of data frames from a list. |
| bunch_translate | Nucleotide to amino acid sequence translation |
| check_distribution | Check that distribution is sums up to one. |
| coding | Working with coding and non-coding clonotype sequences |
| dbAnnotate | Annotate clonotypes using databases |
| dbLoad | Load external immune receptor databases into R |
| dot-quant_column_choice | Get a column's name using the input alias |
| entropy | Information measures |
| filter_barcodes | Filter data by barcodes |
| fixVis | Make publication-ready plots |
| gene_segments | Gene segments table. |
| gene_stats | WIP |
| geneUsage | Gene usage |
| geneUsageAnalysis | Analysis of gene usage |
| getKmers | Kmer analysis of repertoires. |
| group_from_metadata | Get a character vector of samples' groups from the input... |
| has_class | Check class |
| immdata | Immune repertoire dataset |
| immunr_data_format | Specification of the data format used by immunarch... |
| immunr_hclust | Clustering of objects or distance matrices |
| immunr_pca | Dimensionality reduction |
| inc_overlap | Incremental counting of repertoire similarity |
| matrixdiagcopy | Copy the upper matrix triangle to the lower one |
| num_shared_clonotypes | Number of shared clonotypes. |
| overlap_coef | Various measures for overlapping sets of objects. |
| public_matrix | Get a matrix with public clonotype frequencies |
| pubRep | Public repertoire |
| pubRepApply | Apply transformations to public repertoires |
| pubRepFilter | Filter out clonotypes from public repertoires |
| pubRepStatistics | Statistics of number of public clonotypes for each possible... |
| repClonality | Assess clonal proportions of repertoire |
| repDiversity | Estimate diversity of repertoire |
| repExplore | Explore basics of repertoire |
| repLoad | Load repertoire files to the workspace |
| repOverlap | Calculate the overlap between repertoires |
| repOverlapAnalysis | Analysis of overlaps or any distance matrices |
| repSample | Sampling of repertoires |
| repSave | Save repertoire files to the disk. |
| set_pb | Set and update progress bars |
| spectratype | Analyse spectratype of immune repertoires |
| split_immunoseq_files | Split all-samples-in-one ImmunoSEQ files by sample |
| split_to_kmers | Kmers processing. |
| switch_type | Return a column's name |
| top | Get the N most abundant clonotypes |
| trackClonotypes | Clonotype tracking |
| vis | One function to visualise them all |
| vis_bar | Bar plots |
| vis_box | Visualisation of distributions using boxplots |
| vis_circos | Visualisation of matrices using circos plots |
| vis_heatmap | Visualisation of matrices and data frames using ggplot2-based... |
| vis_heatmap2 | Visualisation of matrices using heatmap3-based heatmaps |
| vis_hist | Visualisation of distributions using histograms |
| vis.immunr_chao1 | Visualise diversity. |
| vis.immunr_clonal_prop | Visualise clonality |
| vis.immunr_dynamics | Repertoire dynamics |
| vis.immunr_exp_vol | Visualise exploratory analysis. |
| vis.immunr_gene_usage | Histograms and boxplots (general case / gene usage) |
| vis.immunr_hclust | Visualisation of hierarchical clustering |
| vis.immunr_inc_overlap | Visualise incremental overlaps |
| vis.immunr_kmeans | Visualisation of K-means and DBSCAN clustering |
| vis_immunr_kmer_profile_main | Visualise kmer profiles |
| vis.immunr_kmer_table | Most frequent kmers visualisation. |
| vis.immunr_mds | PCA / MDS / tSNE visualisation (mainly overlap / gene usage) |
| vis.immunr_ov_matrix | Overlap / gene usage distance visualisation |
| vis.immunr_public_repertoire | Public repertoire visualisation |
| vis.immunr_public_statistics | Visualise sharing of clonotypes among samples |
| vis_public_clonotypes | Visualisation of public clonotypes |
| vis_public_frequencies | Public repertoire visualisation |
| vis_radar | Visualisation of distance matrices with polar area plots |
| vis_textlogo | Sequence logo plots for amino acid profiles. |
| vis_treemap | Visualisation of data frames and matrices using treemaps |
