Files in polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

MD5
NEWS.md
NAMESPACE
DESCRIPTION
R/RcppExports.R R/hindhe.R R/data_export.R R/simulation.R R/data_import.R R/classes_methods.R R/pipelines.R R/overdispersion.R R/calculations.R
src/GiniSimpson.cpp
src/RcppExports.cpp
src/BestGenos.cpp
src/AdjustAlleleFreq.cpp
src/ThirdDimProd.cpp
src/PrepVCFexport.cpp
src/SimulateGenotypes.cpp
src/FormatStructure.cpp
src/InitHapAssign.cpp
inst/CITATION
inst/doc/isolocus_sorting.html
inst/doc/polyRADtutorial.R inst/doc/isolocus_sorting.Rmd inst/doc/isolocus_sorting.R
inst/doc/polyRADtutorial.html
inst/doc/polyRADtutorial.Rmd
inst/extdata/DArTag_example.csv
inst/extdata/exampleTASSEL_SAM.txt
inst/extdata/Msi_ploidies.txt
inst/extdata/MsaHindHe2.RData
inst/extdata/ClareMap_alignments.csv
inst/extdata/Msi01genes.vcf.bgz.tbi
inst/extdata/DArTag_example2.csv
inst/extdata/Msi01genes.vcf
inst/extdata/MsaHindHe0.RData
inst/extdata/examplePCA.RData
inst/extdata/ClareMap_HapMap.hmc.txt
inst/extdata/vcfdata.RData
inst/extdata/Msi01genes.vcf.bgz
inst/extdata/example_TagTaxaDist.txt
inst/extdata/DArTag_BLAST_example2.txt
inst/extdata/ClareMap_HapMap.fas.txt
inst/extdata/MsaHindHe.RData
inst/extdata/DArTag_BLAST_example.txt
inst/extdata/MsaHindHe3.RData
inst/extdata/simulate_rad_data.R
inst/python/process_isoloci.py
inst/python/process_sam_multi.py
inst/python/isoloci_fun.py
inst/python/README.md
inst/python/tassel_vcf_tags.py
build/vignette.rds
build/partial.rdb
vignettes/subsetdata.py
vignettes/isolocus_sorting.Rmd
vignettes/overdispersion_inbreeding.png
vignettes/polyRADtutorial.Rmd
data/exampleRAD_mapping.RData
data/exampleRAD.RData
data/Msi01genes.RData
man/GetLikelyGen.Rd man/IterateHWE.Rd man/exampleRAD.Rd man/AddAlleleFreqByTaxa.Rd man/SetBlankTaxa.Rd man/RADdata.Rd man/SubsetByPloidy.Rd man/EstimateContaminationRate.Rd man/AddGenotypePriorProb_ByTaxa.Rd man/AddGenotypePriorProb_Even.Rd man/AddPCA.Rd man/AddAlleleFreqMapping.Rd man/readTASSELGBSv2.Rd man/SubsetByLocus.Rd man/GetTaxa.Rd man/RADdata2VCF.Rd man/AddGenotypePosteriorProb.Rd man/readStacks.Rd man/MergeRareHaplotypes.Rd man/readTagDigger.Rd man/GetWeightedMeanGenotypes.Rd man/reverseComplement.Rd man/AddAlleleLinkages.Rd man/AddGenotypePriorProb_HWE.Rd man/InbreedingFromHindHe.Rd man/MergeTaxaDepth.Rd man/ExpectedHindHe.Rd man/SubsetByTaxon.Rd man/VCF2RADdata.Rd man/readDArTag.Rd man/TestOverdispersion.Rd man/StripDown.Rd man/ExamineGenotype.Rd man/CanDoGetWeightedMeanGeno.Rd man/MakeTasselVcfFilter.Rd man/OneAllelePerMarker.Rd man/readHMC.Rd man/readProcessIsoloci.Rd man/HindHe.Rd man/readProcessSamMulti.Rd man/AddPloidyChiSq.Rd man/AddAlleleFreqHWE.Rd man/AddGenotypeLikelihood.Rd man/AddPloidyLikelihood.Rd man/ExportGAPIT.Rd man/LocusInfo.Rd man/AddGenotypePriorProb_Mapping2Parents.Rd man/PipelineMapping2Parents.Rd man/MergeIdenticalHaplotypes.Rd
man/figures/logo.png
polyRAD documentation built on Nov. 10, 2022, 5:14 p.m.