Toolkit for HLA Immunogenomics
Add an 'AA codon' Line to Alignments When Missing.
Build Sets of Protein, Codon, Coding Nucleotide and Genomic Nucleotide...
Search Alignments for Specific Positions in a Specific Allele
Trim All Versions of HLA Allele Names
Generate a Complete set of Protein, Coding nucleotide and Genomic Nucl...
Identify the Gene-Feature Boundaries in HLA Region Genes
Stratify BIGDAWG Datasets by Specific Alleles
Convert BIGDAWG datasets to PyPop datasetsConverts a BIGDAWG-formatted...
Build Amino Acid, cDNA and gDNA Alignments
Define Categories of Genes Supported by the IPD-IMGT/HLA Database
Describe IPD-IMGT/HLA Database Genes, Identifying Pseudogenes and Gene...
Ensure that AlignType Values are Valid
Identify gDNA Alignments in Which the First Feature Boundary is not Id...
Ensure that Source Values are Valid
Check IPD-IMGT/HLA Release Version Allele Names
Identify Sequence Differences Between Two Alleles at a Locus
Convert Values Across an Entire Data Frame or Vector
Count the Spaces in a Character String
Generate a Customized Peptide, Codon or Nucleotide Sequence Alignment.
Add 'Dot' Delimiters to a Numeric Release Version
Identify and Annotate Gene Features in Pseudogenes and Gene Fragments.
Format PyPop Data Frame Headers
Retrieve Alignment Filenames for HLA Genes
Trim Colon-Delimited HLA Allele Names by Field
Identify the Latest IPD-IMGT/HLA Database Release
GL string code-Integrated Allele Name Translation
Translate GL String to UNIFORMAT
Translate GL Strings to UNIFORMAT Strings
Update a GL String Code to a Specified IPD-IMGT/HLA Database Version
Retrieve Version from Input GL String
Format GL String Code Version Number
Validate a GL String Code
Locate Matches for an Incomplete IPD-IMGT/HLA Database Version
Identify Alleles that Share a Sequence Motif
Generate an Alignment for Specific Alleles at Different Positions
Trim Multiple HLA Allele Names
Translate Multiple GL Strings to UNIFORMAT
Apply validateLocus() to Multiple Loci
Search Multiple Elements of Allele Names Across Release Versions
Search Alignment Sequences at Multiple Positions for a Specified Allel...
Translate a Vector of GL Strings to a Desired IPD-IMGT/HLA Database Ve...
Translate Multiple UNIFORMAT Strings to GL Strings
Update a Vector of GL String Code Data to a Desired IPD-IMGT/HLA Datab...
Identify the Number of Fields in a Colon-Delimited Allele Name
Guides for Parsing the Header Blocks of Alignment Files
Numerical Sort of Alignment Positions that Contain Indels
Convert BIGDAWG File Headers to PyPop Format
Extract Variant Information for Specific Positions in an Alignment
Search Allele Names Across Release Versions
Reintroduce Version Decimals
Calculate Relative Risk for Individual Alleles and Genotypes in BIGDAW...
Convert an AlleleListHistory Release Version to the GitHub Repository ...
Reduce a Release Version to Numerals
Translate HLA Allele Names across IPD-IMGT/HLA Database Release Versio...
Translate a GL String across IPD-IMGT/HLA Database Release Versions
Convert AlignType Values to Source Values
Generate an Alignment for Specific Alleles at Specific Positions
Search Sequences at a Single Position for an Allele
Translate UNIFORMAT to GL String
Translate UNIFORMAT Strings to GL Strings
Update All Package Data Objects Derived from IPD-IMGT/HLA Database Res...
Build the AlleleList History R Object
Update a GL String Code to a Specified IPD-IMGT/HLA Database Version
Validate Allele-Name Format and Presence in HLAalignments
Validate a GL String
Determine if a Locus Name is in the HLAgazetteer
Determine if a Motif is Properly Formatted
Validate the Presence of Variant Positions in an Alignment
Validate a UNIFORMAT String
Validate an IPD-IMGT/HLA Release Version
Builds a Data Frame of Variant Information for Specific Positions in a...
Determine if an Allele Name Ever Existed, and (if so) in Which IPD-IMG...
A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.