Files in Genentech/midasHLA
R package for immunogenomics data handling and association analysis
.BBSoptions
.Rbuildignore
.github/workflows/biocrelease.yaml
.github/workflows/check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENCE
NAMESPACE
NEWS.md
R/asserts.R
R/class.R
R/data.R
R/global.R
R/midasHLA.R
R/parsingFunctions.R
R/stats.R
R/summarise.R
R/transformationFunctions.R
R/utils.R
README.md
data-raw/MiDAS_tut_HLA.R
data-raw/MiDAS_tut_KIR.R
data-raw/MiDAS_tut_object.R
data-raw/MiDAS_tut_pheno.R
data-raw/allele_frequencies.R
data-raw/dict_dist_grantham.R
data-raw/kir_frequencies.R
data/MiDAS_tut_HLA.rda
data/MiDAS_tut_KIR.rda
data/MiDAS_tut_object.rda
data/MiDAS_tut_pheno.rda
data/allele_frequencies.rda
data/dict_dist_grantham.rda
data/kir_frequencies.rda
inst/benchmark/prepareMiDAS_hla_aa.R
inst/benchmark/prepareMiDAS_hla_alleles.R
inst/benchmark/simulateHlaCalls.R
inst/benchmark/workflow_hla_aa.R
inst/benchmark/workflow_hla_alleles.R
inst/extdata/A_prot.Rdata
inst/extdata/B_prot.Rdata
inst/extdata/C_prot.Rdata
inst/extdata/DMA_prot.Rdata
inst/extdata/DMB_prot.Rdata
inst/extdata/DOA_prot.Rdata
inst/extdata/DOB_prot.Rdata
inst/extdata/DPA1_prot.Rdata
inst/extdata/DPB1_prot.Rdata
inst/extdata/DQA1_prot.Rdata
inst/extdata/DQB1_prot.Rdata
inst/extdata/DRA_prot.Rdata
inst/extdata/DRB1_prot.Rdata
inst/extdata/DRB3_prot.Rdata
inst/extdata/DRB4_prot.Rdata
inst/extdata/DRB5_prot.Rdata
inst/extdata/E_prot.Rdata
inst/extdata/F_prot.Rdata
inst/extdata/G_prot.Rdata
inst/extdata/HFE_prot.Rdata
inst/extdata/MICA_prot.Rdata
inst/extdata/MICB_prot.Rdata
inst/extdata/Match_allele_HLA-Bw_only_B.txt
inst/extdata/Match_allele_HLA-C_C1-2.txt
inst/extdata/Match_allele_HLA_Bw.txt
inst/extdata/Match_allele_HLA_Ggroup.txt
inst/extdata/Match_allele_HLA_supertype.txt
inst/extdata/Match_counts_hla_kir_interactions.txt
inst/extdata/Match_counts_kir_haplotypes.txt
inst/extdata/Match_kir_haplotype_gene.txt
inst/extdata/Match_kir_nomenclature_gene.txt
inst/extdata/MiDAS_tut_HLA.txt
inst/extdata/MiDAS_tut_KIR.txt
inst/extdata/MiDAS_tut_pheno.txt
inst/extdata/TAP1_prot.Rdata
inst/extdata/TAP1_prot.fasta
inst/extdata/TAP1_prot.txt
inst/extdata/TAP2_prot.Rdata
inst/extdata/grantham_distance_matrix.tsv
inst/extdata/test_Match_4digit_supertype.txt
inst/extdata/test_aa_variation.Rdata
inst/extdata/test_hla_analyze.Rdata
inst/extdata/test_hla_calls.Rdata
inst/extdata/test_hla_calls_res.Rdata
inst/extdata/test_hla_kir_interactions.Rdata
inst/scripts/download_extdata.R
inst/scripts/parse_alignments.R
longtests/testthat.R
longtests/testthat/test_class.R
longtests/testthat/test_stats.R
man/HWETest.Rd
man/LRTest.Rd
man/MiDAS-class.Rd
man/MiDAS_tut_HLA.Rd
man/MiDAS_tut_KIR.Rd
man/MiDAS_tut_object.Rd
man/MiDAS_tut_pheno.Rd
man/aaVariationToCounts.Rd
man/adjustPValues.Rd
man/allele_frequencies.Rd
man/analyzeAssociations.Rd
man/analyzeConditionalAssociations.Rd
man/applyInheritanceModel.Rd
man/as.data.frame.MiDAS.Rd
man/backquote.Rd
man/characterMatches.Rd
man/checkAlleleFormat.Rd
man/checkColDataFormat.Rd
man/checkHlaCallsFormat.Rd
man/checkKirCallsFormat.Rd
man/checkKirGenesFormat.Rd
man/checkStatisticalModel.Rd
man/colnamesMatches.Rd
man/convertAlleleToVariable.Rd
man/countsToVariables.Rd
man/dfToExperimentMat.Rd
man/dict_dist_grantham.Rd
man/distGrantham.Rd
man/experimentMatToDf.Rd
man/filterByFrequency.Rd
man/filterByOmnibusGroups.Rd
man/filterByVariables.Rd
man/filterExperimentByFrequency.Rd
man/filterExperimentByVariables.Rd
man/filterListByElements.Rd
man/formatResults.Rd
man/getAAFrequencies.Rd
man/getAlleleResolution.Rd
man/getAllelesForAA.Rd
man/getExperimentFrequencies.Rd
man/getExperimentPopulationMultiplicator.Rd
man/getExperiments.Rd
man/getFrequencies.Rd
man/getFrequencyMask.Rd
man/getHlaCalls.Rd
man/getHlaCallsGenes.Rd
man/getHlaFrequencies.Rd
man/getHlaKirInteractions.Rd
man/getKIRFrequencies.Rd
man/getKirCalls.Rd
man/getObjectDetails.Rd
man/getOmnibusGroups.Rd
man/getPlaceholder.Rd
man/getReferenceFrequencies.Rd
man/getVariableAAPos.Rd
man/hasTidyMethod.Rd
man/hlaAlignmentGrantham.Rd
man/hlaCallsGranthamDistance.Rd
man/hlaCallsToCounts.Rd
man/hlaToAAVariation.Rd
man/hlaToVariable.Rd
man/isCharacterOrNULL.Rd
man/isClass.Rd
man/isClassOrNULL.Rd
man/isCountOrNULL.Rd
man/isCountsOrZeros.Rd
man/isExperimentCountsOrZeros.Rd
man/isExperimentInheritanceModelApplicable.Rd
man/isFlagOrNULL.Rd
man/isNumberOrNULL.Rd
man/isStringOrNULL.Rd
man/isTRUEorFALSE.Rd
man/iterativeLRT.Rd
man/iterativeModel.Rd
man/kableResults.Rd
man/kir_frequencies.Rd
man/lapply_tryCatch.Rd
man/listMiDASDictionaries.Rd
man/midasToWide.Rd
man/objectHasPlaceholder.Rd
man/omnibusTest.Rd
man/prepareMiDAS.Rd
man/prepareMiDAS_hla_NK_ligands.Rd
man/prepareMiDAS_hla_aa.Rd
man/prepareMiDAS_hla_alleles.Rd
man/prepareMiDAS_hla_custom.Rd
man/prepareMiDAS_hla_divergence.Rd
man/prepareMiDAS_hla_g_groups.Rd
man/prepareMiDAS_hla_het.Rd
man/prepareMiDAS_hla_kir_interactions.Rd
man/prepareMiDAS_hla_supertypes.Rd
man/prepareMiDAS_kir_custom.Rd
man/prepareMiDAS_kir_genes.Rd
man/prepareMiDAS_kir_haplotypes.Rd
man/readHlaAlignments.Rd
man/readHlaCalls.Rd
man/readKirCalls.Rd
man/reduceAlleleResolution.Rd
man/reduceHlaCalls.Rd
man/runMiDAS.Rd
man/runMiDASGetVarsFreq.Rd
man/stringMatches.Rd
man/summariseAAPosition.Rd
man/updateModel.Rd
man/validateFrequencyCutoffs.Rd
tests/testthat.R
tests/testthat/test_asserts.R
tests/testthat/test_class.R
tests/testthat/test_parsing.R
tests/testthat/test_stats.R
tests/testthat/test_summarise.R
tests/testthat/test_transformation.R
tests/testthat/test_utils.R
vignettes/MiDAS_logo.png
vignettes/MiDAS_tutorial.Rmd
vignettes/MiDAS_vignette.Rmd
