Files in maize-genetics/rTASSEL

R Front-End for TASSEL

.Rbuildignore

.github/.gitignore

.github/CODE_OF_CONDUCT.md .github/CONTRIBUTING.md

.github/workflows/check-standard.yaml

.github/workflows/pkgdown.yaml

.github/workflows/test-coverage.yaml

.gitignore

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NEWS

NEWS.md R/Globals.R R/analysis_association_functions.R R/analysis_diversity_functions.R R/analysis_diversity_vis_functions.R R/analysis_phylogeny_functions.R R/analysis_phylogeny_vis_functions.R R/analysis_relatedness_functions.R R/class_all_generics.R R/class_association_results.R R/class_association_results_sub.R R/class_pca_results.R R/class_tassel_dataset.R R/class_tassel_distance_matrix.R R/data.R R/filter_functions.R R/genomic_prediction.R R/genotype_phenotype_function.R R/genotype_table_functions.R R/imputation_methods.R R/join_methods.R R/logging_support.R R/phenotype_functions.R R/plot_manhattan.R R/plot_manhattan_qc.R R/plot_pca.R R/plot_qq.R R/plot_scree.R R/position_list_functions.R R/taxa_list_functions.R R/utilities_export.R R/utilities_general.R R/utilities_plot_association.R R/zzz.R README.md

_pkgdown.yml

data/rtPaths.rda

inst/CITATION

inst/extdata/maize_chr9_10thin40000.recode.vcf

inst/extdata/mdp_genotype.hmp.txt

inst/extdata/mdp_kinship.txt

inst/extdata/mdp_metadata.csv

inst/extdata/mdp_phenotype.txt

inst/extdata/mdp_population_structure.txt

inst/extdata/mdp_traits.txt

inst/extdata/mdp_traits_nomissing.txt

inst/extdata/rt_sub_chr1.vcf

inst/extdata/rt_sub_chr5.vcf

inst/extdata/wheat_gbs_test.vcf

inst/java/kotlin-stdlib-1.4.32.jar

inst/java/kotlin-stdlib-jdk7-1.4.32.jar

inst/java/kotlin-stdlib-jdk8-1.4.32.jar

inst/java/kotlinx-coroutines-core-jvm-1.4.3.jar

inst/java/lib/ahocorasick-0.2.4.jar

inst/java/lib/biojava-alignment-4.0.0.jar

inst/java/lib/biojava-core-4.0.0.jar

inst/java/lib/biojava-phylo-4.0.0.jar

inst/java/lib/colt-1.2.0.jar

inst/java/lib/commons-codec-1.10.jar

inst/java/lib/commons-math3-3.4.1.jar

inst/java/lib/ejml-core-0.41.jar

inst/java/lib/ejml-ddense-0.41.jar

inst/java/lib/fastutil-8.2.2.jar

inst/java/lib/forester-1.038.jar

inst/java/lib/guava-22.0.jar

inst/java/lib/htsjdk-2.14.0.jar

inst/java/lib/javax.json-1.0.4.jar

inst/java/lib/jcommon-1.0.23.jar

inst/java/lib/jfreesvg-3.2.jar

inst/java/lib/jhdf5-14.12.5.jar

inst/java/lib/json-simple-1.1.1.jar

inst/java/lib/junit-4.10.jar

inst/java/lib/libTasselBlas.dylib

inst/java/lib/log4j-1.2.13.jar

inst/java/lib/mail-1.4.jar

inst/java/lib/slf4j-api-1.7.10.jar

inst/java/lib/slf4j-simple-1.7.10.jar

inst/java/lib/snappy-java-1.1.1.6.jar

inst/java/lib/trove-3.0.3.jar

inst/java/sTASSEL.jar

man/AssociationResults-class.Rd man/AssociationResults-validity.Rd man/AssociationResultsBLUE-class.Rd man/AssociationResultsFast-class.Rd man/AssociationResultsGLM-class.Rd man/AssociationResultsMLM-class.Rd man/PCAResults-class.Rd man/PCAResults-validity.Rd man/TasselDistanceMatrix-class.Rd man/TasselGenotypePhenotype-class.Rd man/as.matrix.TasselDistanceMatrix.Rd man/as.matrix.TasselGenotypePhenotype.Rd man/asTasselDistanceMatrix.Rd man/assocModelFitter.Rd man/associationType.Rd man/colnames-TasselDistanceMatrix-method.Rd man/concatenate.Rd man/createTree.Rd man/dim-TasselDistanceMatrix-method.Rd man/distanceMatrix.Rd man/exportGenotypeTable.Rd

man/figures/archaeopteryx_view.png

man/figures/benchmarks/pltFastAssoc.png

man/figures/benchmarks/pltFeatures.png

man/figures/benchmarks/pltGLMAssoc.png

man/figures/benchmarks/pltKinAll.png

man/figures/benchmarks/pltKinBig.png

man/figures/benchmarks/pltKinSmall.png

man/figures/benchmarks/pltMLMAssoc.png

man/figures/benchmarks/pltVCFImportAll.png

man/figures/benchmarks/pltVCFImportBig.png

man/figures/benchmarks/pltVCFImportSmall.png

man/figures/filter_gr_01.png

man/figures/filter_index_01.png

man/figures/filter_index_02.png

man/figures/filter_pos_01.png

man/figures/filter_pos_02.png

man/figures/filter_site_01.png

man/figures/filter_site_02.png

man/figures/filter_site_03.png

man/figures/filter_site_04.png

man/figures/filter_site_05.png

man/figures/filter_site_06.png

man/figures/filter_taxa_00.png

man/figures/filter_taxa_het.png

man/figures/filter_taxa_na.png

man/figures/filter_taxa_pipe.png

man/figures/filter_taxa_vector.png

man/figures/genotype_table_diagram.png

man/figures/ld_java_viewer.png

man/figures/ld_static.png

man/figures/logo.png

man/figures/manhattan_eh.png

man/filterGenotypeTableBySiteName.Rd man/filterGenotypeTableSites.Rd man/filterGenotypeTableTaxa.Rd man/genomicPrediction.Rd man/getPhenotypeDF.Rd man/getSumExpFromGenotypeTable.Rd man/imputeLDKNNi.Rd man/imputeNumeric.Rd man/intersectJoin.Rd man/kinshipMatrix.Rd man/ldJavaApp.Rd man/ldPlot.Rd man/linkageDiseq.Rd man/mds.Rd man/mergeGenotypeTables.Rd man/ncol-TasselDistanceMatrix-method.Rd man/nrow-TasselDistanceMatrix-method.Rd man/pca.Rd man/plotManhattan.Rd man/plotManhattanQC.Rd man/plotPCA.Rd man/plotQQ.Rd man/plotScree.Rd man/positionList.Rd man/readGenotypePhenotype.Rd man/readGenotypeTableFromGigwa.Rd man/readGenotypeTableFromPath.Rd man/readPhenotypeFromDataFrame.Rd man/readPhenotypeFromPath.Rd man/readTasselDistanceMatrix.Rd man/reportNames.Rd man/rownames-TasselDistanceMatrix-method.Rd man/rtPaths.Rd man/seqDiversity.Rd man/siteSummary.Rd man/startLogger.Rd man/tableReport.Rd man/taxaList.Rd man/taxaSummary.Rd man/traitNames.Rd man/treeJavaApp.Rd man/unionJoin.Rd

pkgdown/favicon/apple-touch-icon-120x120.png

pkgdown/favicon/apple-touch-icon-152x152.png

pkgdown/favicon/apple-touch-icon-180x180.png

pkgdown/favicon/apple-touch-icon-60x60.png

pkgdown/favicon/apple-touch-icon-76x76.png

pkgdown/favicon/apple-touch-icon.png

pkgdown/favicon/favicon-16x16.png

pkgdown/favicon/favicon-32x32.png

pkgdown/favicon/favicon.ico

tests/testthat.R tests/testthat/test_association.R tests/testthat/test_class_association_results.R tests/testthat/test_class_association_results_sub.R tests/testthat/test_class_pca_results.R tests/testthat/test_classes.R tests/testthat/test_export.R tests/testthat/test_filtration.R tests/testthat/test_genomic_prediction.R tests/testthat/test_genotype_coercion.R tests/testthat/test_genotype_table_functions.R tests/testthat/test_gigwa.R tests/testthat/test_imputation.R tests/testthat/test_joining.R tests/testthat/test_ld.R tests/testthat/test_logging.R tests/testthat/test_pca.R tests/testthat/test_phenotype.R tests/testthat/test_phylo_trees.R tests/testthat/test_plot_manhattan.R tests/testthat/test_plot_manhattan_qc.R tests/testthat/test_plot_pca.R tests/testthat/test_plot_qq.R tests/testthat/test_plot_scree.R tests/testthat/test_position_lists.R tests/testthat/test_relatedness.R tests/testthat/test_relatedness_01.R tests/testthat/test_relatedness_02.R tests/testthat/test_seq_diversity.R tests/testthat/test_sum_exp.R tests/testthat/test_taxa_list.R tests/testthat/test_utilities.R tests/testthat/test_utilities_plot_association.R tests/testthat/test_vis_diversity.R tests/testthat/test_vis_phylogeny.R tests/testthat/test_zzz.R vignettes/genotype_filtration.R vignettes/genotype_filtration.Rmd vignettes/rtassel_benchmarks.R vignettes/rtassel_benchmarks.Rmd vignettes/rtassel_installation.R vignettes/rtassel_installation.Rmd vignettes/rtassel_walkthrough.R vignettes/rtassel_walkthrough.Rmd

maize-genetics/rTASSEL documentation built on Nov. 13, 2023, 7:18 a.m.