Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

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**aa_properties:**Tables with amino acid properties**aa_table:**Amino acid / codon table**add_class:**Add a new class attribute**apply_symm:**Apply function to each pair of data frames from a list.**bcrdata:**BCR dataset**bunch_translate:**Nucleotide to amino acid sequence translation**check_distribution:**Check and normalise distributions**coding:**Filter out coding and non-coding clonotype sequences**dbAnnotate:**Annotate clonotypes in immune repertoires using clonotype...**dbLoad:**Load clonotype databases such as VDJDB and McPAS into the R...**dot-quant_column_choice:**Get a column's name using the input alias**entropy:**Information measures**fixVis:**Manipulate ggplot plots and create publication-ready plots**gene_segments:**Gene segments table**gene_stats:**WIP**geneUsage:**Main function for estimation of V-gene and J-gene statistics**geneUsageAnalysis:**Post-analysis of V-gene and J-gene statistics: PCA,...**getKmers:**Calculate the k-mer statistics of immune repertoires**group_from_metadata:**Get a character vector of samples' groups from the input...**has_class:**Check for the specific class**immdata:**Single chain immune repertoire dataset**immunr_data_format:**Specification of the data format used by immunarch dataframes**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**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...**repAlignLineage:**Aligns all sequences incliding germline within each clonal...**repClonalFamily:**Builds a phylogenetic tree using the sequences of a clonal...**repClonality:**Clonality analysis of immune repertoires**repDiversity:**The main function for immune repertoire diversity estimation**repExplore:**Main function for exploratory data analysis: compute the...**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,...**repSample:**Downsampling and resampling of immune repertoires**repSave:**Save immune repertoires to the disk**repSomaticHypermutation:**Calculates number of mutations against the germline for each...**scdata:**Paired chain immune repertoire dataset**select_barcodes:**Select specific clonotypes using barcodes from single-cell...**select_clusters:**Split the immune repertoire data to clusters from single-cell...**seqCluster:**Function for assigning clusters based on sequences similarity**seqDist:**Function for computing distance for sequences**set_pb:**Set and update progress bars**Browse all...**

gene_segments | R Documentation |

Gene segments table

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