Files in olli0601/Phyloscanner.R.utilities
.DS_Store
.Rapp.history
.Rbuildignore
.gitignore
.project
DESCRIPTION
LICENSE
NAMESPACE
Phyloscanner.R.utilities.Rproj
R/.DS_Store
R/phyloscan.fun.R
R/phyloscan.fun.plotting.R
R/phyloscan.fun.private.R
R/phyloscan.fun.scripting.R
README.md
TITLE
articles/Rakai.01.data_description.html
articles/Rakai.02.run_phyloscanner.html
articles/Rakai.03.reconstruct_transmission_networks.html
articles/Rakai.04.direction_of_transmission.html
articles/Stage1.create.read.alignments.html
data/groupM_reference_trees_grubbs1_stats.csv
data/hiv.hxb2.norm.constants.rda
deprecated/phyloscan.Rakai.couples.old.R
deprecated/phyloscan.clustering.R
deprecated/phyloscan.oldfun.R
docs/404.html
docs/LICENSE-text.html
docs/articles/Rakai.01.data_description.html
docs/articles/Rakai.02.run_phyloscanner.html
docs/articles/Rakai.03.reconstruct_transmission_networks.html
docs/articles/Rakai.04.direction_of_transmission.html
docs/articles/Stage1.create.read.alignments.html
docs/articles/figures/Rakai.02.run_phyloscanner.directorystructure.png
docs/articles/figures/Rakai.02.run_phyloscanner.expectedoutput.png
docs/articles/figures/Rakai.03.reconstruct_transmission_networks.rplkl.png
docs/articles/figures/Rakai.03.reconstruct_transmission_networks.rpw.png
docs/articles/figures/Rakai.03.reconstruct_transmission_networks.rtn.png
docs/articles/figures/Rakai.03.reconstruct_transmission_networks.rtnn.png
docs/articles/figures/Stage1.RAxMLArrayscript.png
docs/articles/figures/Stage1.RAxMLscript.png
docs/articles/figures/Stage1.bams.png
docs/articles/figures/Stage1.createbamscmd.png
docs/articles/figures/Stage1.predefinedruns.png
docs/articles/figures/Stage1.sortedbams.png
docs/articles/figures/phsc_analysis_of_dataset_S1_phyloscan_RkA04565F_RkA05315F.png
docs/articles/figures/phsc_analysis_of_dataset_S1_phyloscan_trmchain_34.png
docs/articles/figures/phsc_analysis_of_dataset_S1_phyloscan_trmnetwork_34.png
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/index.html
docs/reference/phsc.bam.get.length.and.pos.of.mergedreads.html
docs/reference/phsc.cmd.bam.calculate.read.distribution.html
docs/reference/phsc.cmd.phyloscanner.multi.html
docs/reference/phsc.cmd.phyloscanner.one.html
docs/reference/phsc.cmd.phyloscanner.one.resume.combinewindows.html
docs/reference/phsc.cmd.phyloscanner.one.resume.html
docs/reference/phsc.cmd.phyloscanner.one.resume.onewindow.html
docs/reference/phsc.cmd.process.phyloscanner.output.in.directory.html
docs/reference/phsc.define.stage1.analyses.html
docs/reference/phsc.find.bam.and.references.html
docs/reference/phsc.find.linked.pairs.html
docs/reference/phsc.find.transmission.networks.from.linked.pairs.html
docs/reference/phsc.get.assignments.by.window.for.couple.html
docs/reference/phsc.get.basic.pairwise.relationships.html
docs/reference/phsc.get.most.likely.transmission.chains.RBGLedmonds.html
docs/reference/phsc.get.most.likely.transmission.chains.greedy.html
docs/reference/phsc.get.most.likely.transmission.chains.html
docs/reference/phsc.get.pairwise.relationships.html
docs/reference/phsc.get.pairwise.relationships.keff.and.neff.html
docs/reference/phsc.get.pairwise.relationships.likelihoods.html
docs/reference/phsc.get.pairwise.relationships.posterior.html
docs/reference/phsc.get.prior.parameter.n0.html
docs/reference/phsc.plot.default.colours.for.relationtypes.html
docs/reference/phsc.plot.maxedge.network.html
docs/reference/phsc.plot.most.likely.transmission.chain.html
docs/reference/phsc.plot.phy.selected.individuals.html
docs/reference/phsc.plot.phy.selected.pairs.html
docs/reference/phsc.plot.phycollapsed.selected.individuals.html
docs/reference/phsc.plot.phyloscan.html
docs/reference/phsc.plot.transmission.network.html
docs/reference/phsc.plot.windowassignments.by.runs.html
docs/reference/phsc.plot.windowsummaries.for.pairs.html
docs/reference/phsc.read.likelytransmissions.html
docs/reference/phsc.read.processed.phyloscanner.output.in.directory.html
docs/reference/phsc.read.subtrees.html
docs/reference/phsc.read.trees.html
docs/reference/raxml.cmd.html
example/ex.cmd.phyloscanner.multi.R
example/ex.cmd.phyloscanner.one.R
example/ex.cmd.phyloscanner.one.resume.R
inst/.DS_Store
inst/HIV1_compendium_AD_B_CPX.fasta
inst/HIV1_compendium_AD_B_CPX_v2.fasta
inst/HIV1_compendium_B.fasta
inst/HIV1_compendium_C_B_CPX.fasta
inst/phsc.pairwise.relationships.Rscript
inst/phsc.read.processed.phyloscanner.output.in.directory.Rscript
man/cmd.iqtree.Rd
man/phsc.bam.get.length.and.pos.of.mergedreads.Rd
man/phsc.cmd.bam.calculate.read.distribution.Rd
man/phsc.cmd.phyloscanner.multi.Rd
man/phsc.cmd.phyloscanner.one.Rd
man/phsc.cmd.phyloscanner.one.resume.Rd
man/phsc.cmd.phyloscanner.one.resume.combinewindows.Rd
man/phsc.cmd.phyloscanner.one.resume.onewindow.Rd
man/phsc.cmd.process.phyloscanner.output.in.directory.Rd
man/phsc.define.stage1.analyses.Rd
man/phsc.find.bam.and.references.Rd
man/phsc.find.linked.pairs.Rd
man/phsc.find.transmission.networks.from.linked.pairs.Rd
man/phsc.get.assignments.by.window.for.couple.Rd
man/phsc.get.basic.pairwise.relationships.Rd
man/phsc.get.most.likely.transmission.chains.RBGLedmonds.Rd
man/phsc.get.most.likely.transmission.chains.Rd
man/phsc.get.most.likely.transmission.chains.greedy.Rd
man/phsc.get.pairwise.relationships.Rd
man/phsc.get.pairwise.relationships.keff.and.neff.Rd
man/phsc.get.pairwise.relationships.likelihoods.Rd
man/phsc.get.pairwise.relationships.posterior.Rd
man/phsc.get.prior.parameter.n0.Rd
man/phsc.plot.default.colours.for.relationtypes.Rd
man/phsc.plot.maxedge.network.Rd
man/phsc.plot.most.likely.transmission.chain.Rd
man/phsc.plot.phy.selected.individuals.Rd
man/phsc.plot.phy.selected.pairs.Rd
man/phsc.plot.phycollapsed.selected.individuals.Rd
man/phsc.plot.phyloscan.Rd
man/phsc.plot.transmission.network.Rd
man/phsc.plot.windowassignments.by.runs.Rd
man/phsc.plot.windowsummaries.for.pairs.Rd
man/phsc.read.likelytransmissions.Rd
man/phsc.read.processed.phyloscanner.output.in.directory.Rd
man/phsc.read.subtrees.Rd
man/phsc.read.trees.Rd
man/raxml.cmd.Rd
misc/.DS_Store
misc/MakePotentialSubpgraphs.yml
misc/define.stage1.analyses.R
misc/find.bam.and.references.R
misc/networks.R
misc/phyloscan.MRCUVRI.scripts.R
misc/phyloscan.Rakai.comparisonstudy.R
misc/phyloscan.Rakai.couples.R
misc/phyloscan.Rakai.gender.R
misc/phyloscan.Rakai.phylogeography.R
misc/phyloscan.TasP.R
misc/phyloscan.codemigration.R
misc/phyloscan.munich.R
misc/phyloscan.projects.R
misc/phyloscan.startme.Rscript
misc/phyloscan.viral.load.project.R
misc/phyloscan.women.with.highdegree.R
misc/phyloscanner_installation.sh
misc/phyloscanner_v1.1.2.tar.gz
misc_data_analysis_RCCS1519/.DS_Store
misc_data_analysis_RCCS1519/Rk1519_01_select_sequences.R
misc_data_analysis_RCCS1519/Rk1519_02_make_potential_transmission_networks.R
misc_data_analysis_RCCS1519/Rk1519_03_make_trees.R
misc_data_analysis_RCCS1519/Rk1519_04_pairwise_relationship.R
misc_data_analysis_RCCS1519/Rk1519_04b_new_find_chains.R
misc_data_analysis_RCCS1519/Rk1519_05_change_threshold.R
misc_data_analysis_RCCS1519/software/TSI_estimate_dates.R
misc_data_analysis_RCCS1519/software/TSI_find_close_to_sero.R
misc_data_analysis_RCCS1519/software/TSI_initialise.R
misc_data_analysis_RCCS1519/software/TSI_initialise_sero2analysis.R
misc_data_analysis_RCCS1519/software/TSI_postprocessing_comparison.R
misc_data_analysis_RCCS1519/software/TSI_run_predictions.R
misc_data_analysis_RCCS1519/software/TSIcalculate_similarity_over_genome.R
misc_data_analysis_RCCS1519/software/TSIcreate_network.R
misc_data_analysis_RCCS1519/software/analyse_trees.R
misc_data_analysis_RCCS1519/software/calculate_similarity.R
misc_data_analysis_RCCS1519/software/calculate_similarity_over_windows.R
misc_data_analysis_RCCS1519/software/check_trees.R
misc_data_analysis_RCCS1519/software/create_network.R
misc_data_analysis_RCCS1519/software/diagnosis.R
misc_data_analysis_RCCS1519/software/find_chains.R
misc_data_analysis_RCCS1519/software/installation.sh
misc_data_analysis_RCCS1519/software/make_deep_sequence_alignments.R
misc_data_analysis_RCCS1519/software/make_trees.R
misc_data_analysis_RCCS1519/software/misc/pangeaid_to_rakairound.R
misc_data_analysis_RCCS1519/software/misc/twosamples_postprocessing.R
misc_data_analysis_RCCS1519/software/notes.md
misc_data_analysis_RCCS1519/software/phylosanner_run.Rmd
misc_data_analysis_RCCS1519/software/phylosanner_run.html
misc_data_analysis_RCCS1519/software/reports/220329_seroconv_study.html
misc_data_analysis_RCCS1519/software/reports/220427_phsc_regression.html
misc_data_analysis_RCCS1519/software/reports/phyloscanner_run.html
misc_data_analysis_RCCS1519/software/run_HIV_TSI.R
misc_data_analysis_RCCS1519/software/runall_TSI.sh
misc_data_analysis_RCCS1519/software/runall_TSI_pairs.sh
misc_data_analysis_RCCS1519/software/runall_TSI_pairs2.sh
misc_data_analysis_RCCS1519/software/runall_TSI_seroconv.sh
misc_data_analysis_RCCS1519/software/runall_TSI_seroconv2.sh
misc_data_analysis_RCCS1519/software/runall_TSI_seroconv2_test.sh
misc_data_analysis_RCCS1519/software/runall_TSI_seroconv2a.sh
misc_data_analysis_RCCS1519/software/runall_TSI_seroconv3.sh
misc_data_analysis_RCCS1519/software/runall_TSI_twosample.sh
misc_data_analysis_RCCS1519/software/utility.R
vignettes/.DS_Store
vignettes/Rakai.01.data_description.Rmd
vignettes/Rakai.02.run_phyloscanner.Rmd
vignettes/Rakai.03.reconstruct_transmission_networks.Rmd
vignettes/Rakai.04.direction_of_transmission.Rmd
vignettes/Seattle.treedater.Rmd
vignettes/Seattle.treedater.html
vignettes/Stage1.create.read.alignments.Rmd
vignettes/figures/.DS_Store
vignettes/figures/Rakai.02.run_phyloscanner.directorystructure.png
vignettes/figures/Rakai.02.run_phyloscanner.expectedoutput.png
vignettes/figures/Rakai.03.reconstruct_transmission_networks.rplkl.png
vignettes/figures/Rakai.03.reconstruct_transmission_networks.rpw.png
vignettes/figures/Rakai.03.reconstruct_transmission_networks.rtn.png
vignettes/figures/Rakai.03.reconstruct_transmission_networks.rtnn.png
vignettes/figures/Rakai.03.reconstruct_transmission_networks.rtp.png
vignettes/figures/Stage1.RAxMLArrayscript.png
vignettes/figures/Stage1.RAxMLscript.png
vignettes/figures/Stage1.bams.png
vignettes/figures/Stage1.createbamscmd.png
vignettes/figures/Stage1.predefinedruns.png
vignettes/figures/Stage1.sortedbams.png
vignettes/figures/phsc_analysis_of_dataset_S1_phyloscan_RkA04565F_RkA05315F.png
vignettes/figures/phsc_analysis_of_dataset_S1_phyloscan_trmchain_34.png
vignettes/figures/phsc_analysis_of_dataset_S1_phyloscan_trmnetwork_34.png
