Files in KathrynCampbell/MADDOG
Lineage Designation and Assignment
.Rbuildignore
.Rhistory
.gitattributes
.gitignore
DESCRIPTION
Datasets/Africa_N/Africa.fasta
Datasets/Africa_N/Africa_N_aligned.fasta
Datasets/Africa_N/Africa_N_metadata.csv
Datasets/Africa_N/Africa_N_sequence_data.csv
Datasets/Arctic_N/Arctic.fasta
Datasets/Arctic_N/Arctic_N_aligned.fasta
Datasets/Arctic_N/Arctic_N_metadata.csv
Datasets/Arctic_N/Arctic_N_sequence_data.csv
Datasets/Asian_N/Asian.fasta
Datasets/Asian_N/Asian_N_aligned.fasta
Datasets/Asian_N/Asian_N_metadata.csv
Datasets/Asian_N/Asian_N_sequence_data.csv
Datasets/Bat_N/Bat.fasta
Datasets/Bat_N/Bat_N_aligned.fasta
Datasets/Bat_N/Bat_N_metadata.csv
Datasets/Bat_N/Bat_N_sequence_data.csv
Datasets/Cosmo_N/Cosmo.fasta
Datasets/Cosmo_N/Cosmo_N_aligned.fasta
Datasets/Cosmo_N/Cosmo_N_metadata.csv
Datasets/Cosmo_N/Cosmo_N_sequence_data.csv
Datasets/Indian_N/Indian.fasta
Datasets/Indian_N/Indian_N_aligned.fasta
Datasets/Indian_N/Indian_N_metadata.csv
Datasets/Indian_N/Indian_N_sequence_data.csv
Datasets/RAC-SK_N/RAC-SK.fasta
Datasets/RAC-SK_N/RAC-SK_N_aligned.fasta
Datasets/RAC-SK_N/RAC-SK_N_metadata.csv
Datasets/RAC-SK_N/RAC-SK_N_sequence_data.csv
Datasets/Vac_N/Vac.fasta
Datasets/Vac_N/Vac_N_aligned.fasta
Datasets/Vac_N/Vac_N_metadata.csv
Datasets/Vac_N/Vac_N_sequence_data.csv
Diego/AM5.csv
Diego/AM5.fasta
Diego/AM5_corrected.fasta
Diego/Diego_metadata.csv
Diego/diego.fasta
Diego/new_AM.csv
Diego/new_AM.fasta
Example_assignment/Example_assignment.fasta
Example_designation/Example_designation.fasta
Example_designation/Example_designation_metadata.csv
MADDOG.Rproj
NAMESPACE
R/assign_lineages.R
R/lineage_info.R
R/lineage_tree.r
R/mafft_reorder.R
R/node_info.r
R/node_info_nolength.R
R/reference_creation.R
R/seq_designation.r
R/seq_designation_nolength.R
R/sunburst_function.r
README.md
Run/.Rhistory
Run/additions2.R
Run/additions3.1.R
Run/node_info_nolength.R
Run/run_designation.R
Run/run_markdown.R
Run/seq_designation_nolength.R
Run/windows_run_assignment.R
assignment.sh
designation.sh
designation2.sh
environment.yml
inst/extdata/Examples/Lineage_assignment/example.fasta
inst/extdata/Examples/Lineage_designation/Example_designation_aligned.fasta
inst/extdata/Examples/Lineage_designation/Example_designation_aligned.fasta.contree
inst/extdata/Examples/Lineage_designation/Example_designation_metadata.csv
inst/extdata/Examples/Lineage_designation/ancestral_sequences.fasta
inst/extdata/References/RABV/lineage_info.csv
inst/extdata/References/RABV/reference_aligned.fasta
inst/extdata/References/RABV/reference_aligned_old.fasta
inst/extdata/References/RABV/reference_aligned_old.fasta.contree
inst/extdata/References/RABV/reference_clusters.csv
inst/extdata/References/RABV/seq.fasta
inst/extdata/updates.eml
man/assign_lineages.Rd
man/lineage_info.Rd
man/lineage_tree.Rd
man/mafft_reorder.Rd
man/node_info.Rd
man/seq_designation.Rd
man/sunburst.Rd
new_AM/Alignment/new_AM_combined_aligned.fasta
new_AM/Assignment/assignment.csv
new_AM/Figures/new_AM_lineage_tree.png
new_AM/Figures/new_AM_sunburst.html
new_AM/Outputs/emerging_undersampled.csv
new_AM/Outputs/new_lineages.csv
new_AM/Outputs/relevant_lineages.csv
new_AM/Outputs/sequence_data.csv
new_AM/Outputs/singleton_details.csv
new_AM/Outputs/singletons_of_interest.csv
new_AM/Report/report.html
new_AM/Report/report_files/bootstrap-3.3.5/css/bootstrap-theme.css
new_AM/Report/report_files/bootstrap-3.3.5/css/bootstrap-theme.css.map
new_AM/Report/report_files/bootstrap-3.3.5/css/bootstrap-theme.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/bootstrap.css
new_AM/Report/report_files/bootstrap-3.3.5/css/bootstrap.css.map
new_AM/Report/report_files/bootstrap-3.3.5/css/bootstrap.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/cerulean.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/cosmo.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/darkly.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/flatly.min.css
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new_AM/Report/report_files/bootstrap-3.3.5/css/fonts/OpenSansLight.ttf
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new_AM/Report/report_files/bootstrap-3.3.5/css/sandstone.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/simplex.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/spacelab.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/united.min.css
new_AM/Report/report_files/bootstrap-3.3.5/css/yeti.min.css
new_AM/Report/report_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
new_AM/Report/report_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.svg
new_AM/Report/report_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.ttf
new_AM/Report/report_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
new_AM/Report/report_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
new_AM/Report/report_files/bootstrap-3.3.5/js/bootstrap.js
new_AM/Report/report_files/bootstrap-3.3.5/js/bootstrap.min.js
new_AM/Report/report_files/bootstrap-3.3.5/js/npm.js
new_AM/Report/report_files/bootstrap-3.3.5/shim/html5shiv.min.js
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new_AM/Report/report_files/crosstalk-1.2.0/js/crosstalk.js
new_AM/Report/report_files/crosstalk-1.2.0/js/crosstalk.js.map
new_AM/Report/report_files/crosstalk-1.2.0/js/crosstalk.min.js
new_AM/Report/report_files/crosstalk-1.2.0/js/crosstalk.min.js.map
new_AM/Report/report_files/crosstalk-1.2.0/scss/crosstalk.scss
new_AM/Report/report_files/figure-html/years_graph-1.png
new_AM/Report/report_files/header-attrs-2.22/header-attrs.js
new_AM/Report/report_files/htmlwidgets-1.6.2/htmlwidgets.js
new_AM/Report/report_files/jquery-3.6.0/jquery-3.6.0.js
new_AM/Report/report_files/jquery-3.6.0/jquery-3.6.0.min.js
new_AM/Report/report_files/jquery-3.6.0/jquery-3.6.0.min.map
new_AM/Report/report_files/jqueryui-1.13.2/AUTHORS.txt
new_AM/Report/report_files/jqueryui-1.13.2/LICENSE.txt
new_AM/Report/report_files/jqueryui-1.13.2/images/ui-icons_444444_256x240.png
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new_AM/Report/report_files/jqueryui-1.13.2/index.html
new_AM/Report/report_files/jqueryui-1.13.2/jquery-ui.css
new_AM/Report/report_files/jqueryui-1.13.2/jquery-ui.js
new_AM/Report/report_files/jqueryui-1.13.2/jquery-ui.min.css
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new_AM/Report/report_files/jqueryui-1.13.2/jquery-ui.structure.css
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new_AM/Report/report_files/jqueryui-1.13.2/jquery-ui.theme.css
new_AM/Report/report_files/jqueryui-1.13.2/jquery-ui.theme.min.css
new_AM/Report/report_files/navigation-1.1/codefolding-lua.css
new_AM/Report/report_files/navigation-1.1/codefolding.js
new_AM/Report/report_files/navigation-1.1/sourceembed.js
new_AM/Report/report_files/navigation-1.1/tabsets.js
new_AM/Report/report_files/pagedtable-1.1/css/pagedtable.css
new_AM/Report/report_files/pagedtable-1.1/js/pagedtable.js
new_AM/Report/report_files/plotly-binding-4.10.2/plotly.js
new_AM/Report/report_files/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
new_AM/Report/report_files/plotly-main-2.11.1/plotly-latest.min.js
new_AM/Report/report_files/tocify-1.9.1/jquery.tocify.css
new_AM/Report/report_files/tocify-1.9.1/jquery.tocify.js
new_AM/Report/report_files/typedarray-0.1/typedarray.min.js
new_AM/Report/troupin.png
new_AM/Timetree/ancestral_sequences.fasta
new_AM/Timetree/annotated_tree.nexus
new_AM/Timetree/auspice_tree.json
new_AM/Timetree/branch_mutations.txt
new_AM/Timetree/sequence_evolution_model.txt
new_AM/Trees/new_AM_combined_aligned.fasta.bionj
new_AM/Trees/new_AM_combined_aligned.fasta.ckp.gz
new_AM/Trees/new_AM_combined_aligned.fasta.contree
new_AM/Trees/new_AM_combined_aligned.fasta.iqtree
new_AM/Trees/new_AM_combined_aligned.fasta.log
new_AM/Trees/new_AM_combined_aligned.fasta.mldist
new_AM/Trees/new_AM_combined_aligned.fasta.splits.nex
new_AM/Trees/new_AM_combined_aligned.fasta.treefile
new_AM/Trees/new_AM_combined_aligned.fasta.uniqueseq.phy
new_AM/new_AM.fasta
new_AM/new_AM_combined_metadata.csv
new_AM/new_AM_metadata.csv
new_designation.sh
report.rmd
report.sh
troupin.png
vignettes/.build.timestamp
vignettes/designation_and_assignment.Rmd
