Files in lvclark/polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/RcppExports.R
R/calculations.R
R/classes_methods.R
R/data_export.R
R/data_import.R
R/hindhe.R
R/overdispersion.R
R/pipelines.R
R/simulation.R
README.md
code_of_conduct.md
data/Msi01genes.RData
data/exampleRAD.RData
data/exampleRAD_mapping.RData
inst/CITATION
inst/extdata/ClareMap_HapMap.fas.txt
inst/extdata/ClareMap_HapMap.hmc.txt
inst/extdata/ClareMap_alignments.csv
inst/extdata/DArTag_BLAST_example.txt
inst/extdata/DArTag_BLAST_example2.txt
inst/extdata/DArTag_example.csv
inst/extdata/DArTag_example2.csv
inst/extdata/MsaHindHe.RData
inst/extdata/MsaHindHe0.RData
inst/extdata/MsaHindHe2.RData
inst/extdata/MsaHindHe3.RData
inst/extdata/Msi01genes.vcf
inst/extdata/Msi01genes.vcf.bgz
inst/extdata/Msi01genes.vcf.bgz.tbi
inst/extdata/Msi_ploidies.txt
inst/extdata/examplePCA.RData
inst/extdata/exampleTASSEL_SAM.txt
inst/extdata/example_TagTaxaDist.txt
inst/extdata/simulate_rad_data.R
inst/extdata/vcfdata.RData
inst/python/README.md
inst/python/isoloci_fun.py
inst/python/process_isoloci.py
inst/python/process_sam_multi.py
inst/python/tassel_vcf_tags.py
man/AddAlleleFreqByTaxa.Rd
man/AddAlleleFreqHWE.Rd
man/AddAlleleFreqMapping.Rd
man/AddAlleleLinkages.Rd
man/AddGenotypeLikelihood.Rd
man/AddGenotypePosteriorProb.Rd
man/AddGenotypePriorProb_ByTaxa.Rd
man/AddGenotypePriorProb_Even.Rd
man/AddGenotypePriorProb_HWE.Rd
man/AddGenotypePriorProb_Mapping2Parents.Rd
man/AddPCA.Rd
man/AddPloidyChiSq.Rd
man/AddPloidyLikelihood.Rd
man/CanDoGetWeightedMeanGeno.Rd
man/EstimateContaminationRate.Rd
man/ExamineGenotype.Rd
man/ExpectedHindHe.Rd
man/ExportGAPIT.Rd
man/GetLikelyGen.Rd
man/GetTaxa.Rd
man/GetWeightedMeanGenotypes.Rd
man/HindHe.Rd
man/InbreedingFromHindHe.Rd
man/IterateHWE.Rd
man/LocusInfo.Rd
man/MakeTasselVcfFilter.Rd
man/MergeIdenticalHaplotypes.Rd
man/MergeRareHaplotypes.Rd
man/MergeTaxaDepth.Rd
man/OneAllelePerMarker.Rd
man/PipelineMapping2Parents.Rd
man/RADdata.Rd
man/RADdata2VCF.Rd
man/SetBlankTaxa.Rd
man/StripDown.Rd
man/SubsetByLocus.Rd
man/SubsetByPloidy.Rd
man/SubsetByTaxon.Rd
man/TestOverdispersion.Rd
man/VCF2RADdata.Rd
man/exampleRAD.Rd
man/figures/logo.png
man/readDArTag.Rd
man/readHMC.Rd
man/readProcessIsoloci.Rd
man/readProcessSamMulti.Rd
man/readStacks.Rd
man/readTASSELGBSv2.Rd
man/readTagDigger.Rd
man/reverseComplement.Rd
pull_request_template.md
src/AdjustAlleleFreq.cpp
src/BestGenos.cpp
src/FormatStructure.cpp
src/GiniSimpson.cpp
src/InitHapAssign.cpp
src/PrepVCFexport.cpp
src/RcppExports.cpp
src/SimulateGenotypes.cpp
src/ThirdDimProd.cpp
vignettes/isolocus_sorting.Rmd
vignettes/isolocus_sorting.html
vignettes/overdispersion_inbreeding.png
vignettes/polyRADtutorial.Rmd
vignettes/polyRADtutorial.html
vignettes/render_vignettes.R
vignettes/subsetdata.py
