Immunoglobulin Clonal Lineage and Diversity Analysis
Build a DNA distance matrix
Build an AA distance matrix
Amino acid abbreviation translations
S4 class defining a clonal abundance curve
alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis
The Alakazam package
Calculates the aliphatic index of amino acid sequences
Calculate clonal alpha diversity
Calculates amino acid chemical properties for sequence data
Standard ggplot settings
Infer an Ig lineage using PHYLIP
Calculates the average bulkiness of amino acid sequences
Calculate sample coverage
Calculate the diversity index
S4 class defining a clone
Calculates the net charge of amino acid sequences.
Check data.frame for valid columns and issue message if invalid
Remove duplicate DNA sequences and combine annotations
Combine IgPhyML object parameters into a dataframe
Tabulates clones sizes
Tabulates V(D)J allele, gene or family usage.
Count sequence patterns
Available CPU cores
Default colors
S4 class defining a diversity curve
S4 class defining edge significance
Estimates the complete clonal relative abundance distribution
Extracts FWRs and CDRs from IMGT-gapped sequences
Retrieve the first non-root node of a lineage tree
Calculate path lengths from the tree root
Get a data.frame with sequencing qualities per position
Get Ig segment allele, gene and family names
Convert a tree in igraph graph format to ape phylo format.
Calculates the hydrophobicity of amino acid sequences
Plot multiple ggplot objects
Group sequences by gene assignment
IMGT V-segment regions
Validate amino acid sequences
IUPAC ambiguous characters
Calculate junction region alignment properties
Generate a ChangeoClone object for lineage construction
Create a temporary folder
Mask sequence positions with low quality
Masks ragged leading and trailing edges of aligned DNA sequences
Masks gap characters in DNA sequences
S4 class defining edge significance
Calculate pairwise distances between sequences
Pads ragged ends of aligned DNA sequences
Calculate pairwise distances between sequences
Calculate pairwise equivalence between sequences
Permute the node labels of a tree
Convert a tree in ape phylo format to igraph graph format.
Plot a clonal abundance distribution
Plot the results of alphaDiversity
Plot the results of diversity testing
Plot the results of an edge permutation test
Plot the results of a founder permutation test
Plots subtree statistics for multiple trees
Calculates the average polarity of amino acid sequences
Standard progress bar
Generate a clonal diversity index curve
Read a Change-O tab-delimited database file
Load sequencing quality scores from a FASTQ file
Read in output from IgPhyML
Calculate distance between two sequences
Test DNA sequences for equality.
Sort V(D)J genes
Weighted meta-analysis of p-values via Stouffer's method
Generate subtree summary statistics for a tree
Tabulate the number of edges between annotations within a lineage tree
Pairwise test of the diversity index
Tests for parent-child annotation enrichment in lineage trees
Tests for MRCA annotation enrichment in lineage trees
Translate nucleotide sequences to amino acids
Translate a vector of strings
Write a Change-O tab-delimited database file
Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.