| addCodonLine | Add an 'AA codon' Line to Alignments When Missing. |
| alignmentFull | Build Sets of Protein, Codon, Coding Nucleotide and Genomic... |
| alignmentSearch | Search Alignments for Specific Positions in a Specific Allele |
| alleleListHistory | Allele Names Across All Release Versions |
| alleleTrim | Trim All Versions of HLA Allele Names |
| atlasFull | Generate a Complete set of Protein, Coding nucleotide and... |
| atlasMaker | Identify the Gene-Feature Boundaries in HLA Region Genes |
| BDstrat | Stratify BIGDAWG Datasets by Specific Alleles |
| BDtoPyPop | Convert BIGDAWG datasets to PyPop datasets Converts a... |
| buildAlignments | Build Amino Acid, cDNA and gDNA Alignments |
| buildGazeteer | Define Categories of Genes Supported by the IPD-IMGT/HLA... |
| buildIMGTHLAGeneTypes | Describe IPD-IMGT/HLA Database Genes, Identifying Pseudogenes... |
| checkAlignType | Ensure that AlignType Values are Valid |
| checkgDNAstart | Identify gDNA Alignments in Which the First Feature Boundary... |
| checkSource | Ensure that Source Values are Valid |
| checkVersion | Check IPD-IMGT/HLA Release Version Allele Names |
| compareSequences | Identify Sequence Differences Between Two Alleles at a Locus |
| convertAny | Convert Values Across an Entire Data Frame or Vector |
| countSpaces | Count the Spaces in a Character String |
| customAlign | Generate a Customized Peptide, Codon or Nucleotide Sequence... |
| expandVersion | Add 'Dot' Delimiters to a Numeric Release Version |
| ffN | Identify and Annotate Gene Features in Pseudogenes and Gene... |
| formatHead | Format PyPop Data Frame Headers |
| fragmentFeatureNames | Gene Features of HLA Pseudogenes and Gene Fragments |
| getAlignmentNames | Retrieve Alignment Filenames for HLA Genes |
| getField | Trim Colon-Delimited HLA Allele Names by Field |
| getLatestVersion | Identify the Latest IPD-IMGT/HLA Database Release |
| GIANT | GL string code-Integrated Allele Name Translation |
| GLSC.ex | Example Data Frame of Genotype List String Code Data |
| GLStoUNI | Translate GL String to UNIFORMAT |
| GLstring.ex | Example Data Frame of Genotype List String Data. |
| GLtoUN | Translate GL Strings to UNIFORMAT Strings |
| GLupdate | Update a GL String Code to a Specified IPD-IMGT/HLA Database... |
| GLV | Retrieve Version from Input GL String |
| GLV2 | Format GL String Code Version Number |
| GLvalidate | Validate a GL String Code |
| GLVhelper | Locate Matches for an Incomplete IPD-IMGT/HLA Database... |
| HLAatlas | Boundary Positions of Exons, Introns and UTRs in Amino Acid,... |
| HLAgazeteer | Functional and Organizational Categories of Genes Supported... |
| IMGTHLAGeneTypes | Molecular characteristics of the Genes Curated by the... |
| motifMatch | Identify Alleles that Share a Sequence Motif |
| multiAlign | Generate an Alignment for Specific Alleles at Different... |
| multiAlleleTrim | Trim Multiple HLA Allele Names |
| multiGLStoUNI | Translate Multiple GL Strings to UNIFORMAT |
| multiLocusValidation | Apply validateLocus() to Multiple Loci |
| multiQueryRelease | Search Multiple Elements of Allele Names Across Release... |
| multiSearch | Search Alignment Sequences at Multiple Positions for a... |
| multiTranslateGLstring | Translate a Vector of GL Strings to a Desired IPD-IMGT/HLA... |
| multiUNItoGLS | Translate Multiple UNIFORMAT Strings to GL Strings |
| multiUpdateGL | Update a Vector of GL String Code Data to a Desired... |
| numFields | Identify the Number of Fields in a Colon-Delimited Allele... |
| parseAlignmentHead | Guides for Parsing the Header Blocks of Alignment Files |
| posSort | Numerical Sort of Alignment Positions that Contain Indels |
| pypopHeaders | Convert BIGDAWG File Headers to PyPop Format |
| queryPositions | Extract Variant Information for Specific Positions in an... |
| queryRelease | Search Allele Names Across Release Versions |
| redec | Reintroduce Version Decimals |
| relRisk | Calculate Relative Risk for Individual Alleles and Genotypes... |
| repoVersion | Convert an AlleleListHistory Release Version to the GitHub... |
| sHLAdata | Synthetic HLA Data for use with Package Examples |
| squashVersion | Reduce a Release Version to Numerals |
| translateAllele | Translate HLA Allele Names across IPD-IMGT/HLA Database... |
| translateGLstring | Translate a GL String across IPD-IMGT/HLA Database Release... |
| typeToSource | Convert AlignType Values to Source Values |
| uniAlign | Generate an Alignment for Specific Alleles at Specific... |
| UNIFORMAT.example | Example Data Frame of UNIFORMAT Data. |
| uniSearch | Search Sequences at a Single Position for an Allele |
| UNItoGLS | Translate UNIFORMAT to GL String |
| UNtoGL | Translate UNIFORMAT Strings to GL Strings |
| updateAll | Update All Package Data Objects Derived from IPD-IMGT/HLA... |
| updateAlleleListHistory | Build the AlleleList History R Object |
| updateGL | Update a GL String Code to a Specified IPD-IMGT/HLA Database... |
| validateAllele | Validate Allele-Name Format and Presence in HLAalignments |
| validateGLstring | Validate a GL String |
| validateLocus | Determine if a Locus Name is in the HLAgazeteer |
| validateMotif | Determine if a Motif is Properly Formatted |
| validatePositions | Validate the Presence of Variant Positions in an Alignment |
| validateUniformat | Validate a UNIFORMAT String |
| validateVersion | Validate an IPD-IMGT/HLA Release Version |
| variantTable | Builds a Data Frame of Variant Information for Specific... |
| verifyAllele | Determine if an Allele Name Ever Existed, and (if so) in... |
