maize-genetics/rPHG
R front-end for the practical haplotype graph

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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
maize-genetics/rPHG documentation built on April 4, 2024, 11:18 p.m.

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