Files in maize-genetics/rPHG
R front-end for the practical haplotype graph
.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS
NEWS.md
R/class_all_generics.R
R/class_haplotype_graph.R
R/class_phg_con.R
R/class_phg_con_local.R
R/class_phg_con_server.R
R/class_phg_dataset.R
R/class_phg_method.R
R/constants.R
R/logging_support.R
R/method_table.R
R/read_hap_ids.R
R/read_phg_dataset.R
R/read_ref_ranges.R
R/read_samples.R
R/stats_gvcf_metrics.R
R/stats_mutual_info.R
R/stats_num_haplotypes.R
R/stats_taxa_by_node.R
R/utilities_api_brapi.R
R/utilities_api_phg.R
R/utilities_general.R
R/utilities_stats.R
R/vis_plot_dot.R
R/vis_plot_graph.R
R/vis_plot_mutual_info.R
R/zzz.R
README.md
_pkgdown.yml
inst/extdata/configSQLite.txt
inst/extdata/dummy_anchors_small.anchorspro
inst/extdata/gvcf/dummy.gvcf.gz
inst/extdata/gvcf/dummy.gvcf.gz.tbi
inst/extdata/phg_smallseq_test.db
inst/java/ahocorasick-0.2.4.jar
inst/java/biojava-alignment-6.0.4.jar
inst/java/biojava-core-6.0.4.jar
inst/java/biojava-genome-6.0.4.jar
inst/java/biojava-phylo-4.2.12.jar
inst/java/colt-1.2.0.jar
inst/java/commons-codec-1.10.jar
inst/java/commons-io-2.11.0.jar
inst/java/commons-math3-3.4.1.jar
inst/java/ejml-core-0.41.jar
inst/java/ejml-ddense-0.41.jar
inst/java/enzymes.ini
inst/java/error_prone_annotations-2.19.1.jar
inst/java/fastutil-8.2.2.jar
inst/java/forester-1.039.jar
inst/java/gs-core-1.3.jar
inst/java/gs-ui-1.3.jar
inst/java/guava-22.0.jar
inst/java/htsjdk-2.24.1.jar
inst/java/ini4j-0.5.4.jar
inst/java/itextpdf-5.1.0.jar
inst/java/jackson-annotations-2.13.2.jar
inst/java/jackson-core-2.13.2.jar
inst/java/jackson-databind-2.13.2.2.jar
inst/java/jackson-module-kotlin-2.13.2.jar
inst/java/javax.json-1.0.4.jar
inst/java/jcommon-1.0.23.jar
inst/java/jfreechart-1.0.19.jar
inst/java/jfreesvg-3.2.jar
inst/java/jhdf5-14.12.5.jar
inst/java/json-simple-1.1.1.jar
inst/java/junit-4.10.jar
inst/java/kotlin-reflect-1.6.10.jar
inst/java/kotlin-stdlib-1.6.10.jar
inst/java/kotlin-stdlib-jdk7-1.6.10.jar
inst/java/kotlin-stdlib-jdk8-1.6.10.jar
inst/java/kotlinx-coroutines-core-jvm-1.6.0.jar
inst/java/libTasselBlas.dylib
inst/java/log4j-1.2.13.jar
inst/java/mail-1.4.jar
inst/java/phg.jar
inst/java/postgresql-9.4-1201.jdbc41.jar
inst/java/protobuf-java-3.23.0.jar
inst/java/protobuf-java-util-3.23.0.jar
inst/java/protobuf-kotlin-3.23.0.jar
inst/java/sTASSEL.jar
inst/java/scala-library-2.10.1.jar
inst/java/slf4j-api-1.7.10.jar
inst/java/slf4j-simple-1.7.10.jar
inst/java/snappy-java-1.1.8.4.jar
inst/java/sqlite-jdbc-3.39.2.1.jar
inst/java/sshj-0.32.0.jar
inst/java/trove-3.0.3.jar
man/HaplotypeGraph-class.Rd
man/HaplotypeGraph-validity.Rd
man/PHGCon-class.Rd
man/PHGCon-validity.Rd
man/PHGDataSet-class.Rd
man/PHGLocalCon-class.Rd
man/PHGLocalCon-validity.Rd
man/PHGLocalCon.Rd
man/PHGMethod-class.Rd
man/PHGMethod-validity.Rd
man/PHGMethod.Rd
man/PHGServerCon-class.Rd
man/PHGServerCon-validity.Rd
man/PHGServerCon.Rd
man/brapiURL.Rd
man/brapiVersion.Rd
man/buildHaplotypeGraph.Rd
man/calcMutualInfo.Rd
man/configFilePath.Rd
man/dbName.Rd
man/dbType.Rd
man/figures/logo.png
man/gvcfMetrics.Rd
man/host.Rd
man/httProtocol.Rd
man/isDemo.Rd
man/javaMemoryAddress.Rd
man/javaRefObj.Rd
man/json2tibble.Rd
man/numHaploPerRefRange.Rd
man/numberOfChromosomes.Rd
man/numberOfNodes.Rd
man/numberOfRefRanges.Rd
man/numberOfTaxa.Rd
man/phgConObj.Rd
man/phgMethodId.Rd
man/phgMethodType.Rd
man/phgType.Rd
man/plotDot.Rd
man/plotGraph.Rd
man/plotMutualInfo.Rd
man/port.Rd
man/readHaplotypeIds.Rd
man/readPHGDataSet.Rd
man/readRefRanges.Rd
man/readSamples.Rd
man/serverInfo.Rd
man/show.Rd
man/showPHGMethods.Rd
man/startLogger.Rd
man/taxaByNode.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_class_all_generics.R
tests/testthat/test_class_haplotype_graph.R
tests/testthat/test_class_phg_con.R
tests/testthat/test_class_phg_con_local.R
tests/testthat/test_class_phg_con_server.R
tests/testthat/test_class_phg_dataset.R
tests/testthat/test_class_phg_method.R
tests/testthat/test_gvcf_metric.R
tests/testthat/test_logging_support.R
tests/testthat/test_stats_taxa_by_node.R
tests/testthat/test_utilities_api_brapi.R
tests/testthat/test_utilities_api_phg.R
tests/testthat/test_utilities_general.R
tests/testthat/test_utilities_stats.R
tests/testthat/test_vis_plot_dot.R
tests/testthat/test_vis_plot_graph.R
tests/testthat/test_vis_plot_mutual_info.R
tests/testthat/test_zzz.R
vignettes/img/corrplot_example.png
vignettes/img/num_hap_plot.png
vignettes/img/rphg_data_structure.png
vignettes/img/visnetwork_01.png
vignettes/img/visnetwork_02.png
vignettes/img/visnetwork_03.png
vignettes/rphg_config_files.R
vignettes/rphg_config_files.Rmd
vignettes/rphg_installation.R
vignettes/rphg_installation.Rmd
vignettes/rphg_walkthrough.R
vignettes/rphg_walkthrough.Rmd
