A B C D E F G H I J K M N O P R S T V misc
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 |
bunch_translate | Nucleotide to amino acid sequence translation |
chao1 | 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 |
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 | Main function for immune repertoire diversity estimation |
entropy | Information measures |
fixVis | Manipulate ggplot plots and make publication-ready plots |
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 kmer tatistics of immune repertoires |
getKmers | Calculate the kmer tatistics 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 | Main function for immune repertoire diversity estimation |
gini_simpson | Main function for immune repertoire diversity estimation |
group_from_metadata | Get a character vector of samples' groups from the input metadata file |
has_class | Check for the specific class |
hill_numbers | Main function for immune repertoire diversity estimation |
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 |
inc_overlap | Incremental counting of repertoire similarity |
inframes | Filter out coding and non-coding clonotype sequences |
inverse_simpson | Main function for immune repertoire diversity estimation |
js_div | Information measures |
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. |
makeKmerTable | Calculate the kmer tatistics of immune repertoires |
matrixdiagcopy | Copy the upper matrix triangle to the lower one |
noncoding | Filter out coding and non-coding clonotype sequences |
outofframes | Filter out coding and non-coding clonotype sequences |
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 |
rarefaction | Main function for immune repertoire diversity estimation |
rare_proportion | Clonality analysis of immune repertoires |
repClonality | Clonality analysis of immune repertoires |
repDiversity | Main function for immune repertoire diversity estimation |
repExplore | Main function for exploratory data analysis: compute the distribution of lengths, clones, etc. |
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 |
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 |
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 |
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 |
vis | One function to visualise them all |
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_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. |
.quant_column_choice | Get a column's name using the input alias |