Files in KopfLab/turnoveR
Processing tools for protein degradation experiments.
.Rbuildignore
.gitignore
DESCRIPTION
Makefile
NAMESPACE
R/counts.R
R/kegg.R
R/package.R
R/protein_degradation.R
R/svm_data.R
R/uniprot.R
R/utilities.R
R/visualization.R
README.Rmd
README.md
_pkgdown.yml
docs/CNAME
docs/articles/analysis_demo.html
docs/articles/data_processing.html
docs/articles/data_processing_files/DiagrammeR-binding-1.0.0/DiagrammeR.js
docs/articles/data_processing_files/DiagrammeR-styles-0.2/styles.css
docs/articles/data_processing_files/chromatography-0.1/LICENSE
docs/articles/data_processing_files/chromatography-0.1/chromatography.js
docs/articles/data_processing_files/crosstalk-1.0.0/css/crosstalk.css
docs/articles/data_processing_files/crosstalk-1.0.0/js/crosstalk.js
docs/articles/data_processing_files/crosstalk-1.0.0/js/crosstalk.js.map
docs/articles/data_processing_files/crosstalk-1.0.0/js/crosstalk.min.js
docs/articles/data_processing_files/crosstalk-1.0.0/js/crosstalk.min.js.map
docs/articles/data_processing_files/d3-3.3.8/LICENSE
docs/articles/data_processing_files/d3-3.3.8/d3.min.js
docs/articles/data_processing_files/dagre-0.4.0/LICENSE
docs/articles/data_processing_files/dagre-0.4.0/dagre-d3.min.js
docs/articles/data_processing_files/figure-html/unnamed-chunk-14-1.png
docs/articles/data_processing_files/figure-html/unnamed-chunk-15-1.png
docs/articles/data_processing_files/figure-html/unnamed-chunk-16-1.png
docs/articles/data_processing_files/figure-html/unnamed-chunk-19-1.png
docs/articles/data_processing_files/htmlwidgets-1.1/htmlwidgets.js
docs/articles/data_processing_files/jquery-1.11.3/jquery-AUTHORS.txt
docs/articles/data_processing_files/jquery-1.11.3/jquery.js
docs/articles/data_processing_files/jquery-1.11.3/jquery.min.js
docs/articles/data_processing_files/jquery-1.11.3/jquery.min.map
docs/articles/data_processing_files/mermaid-0.3.0/LICENSE
docs/articles/data_processing_files/mermaid-0.3.0/dist/mermaid.css
docs/articles/data_processing_files/mermaid-0.3.0/dist/mermaid.slim.min.js
docs/articles/data_processing_files/pagedtable-1.1/css/pagedtable.css
docs/articles/data_processing_files/pagedtable-1.1/js/pagedtable.js
docs/articles/data_processing_files/plotly-binding-4.7.1/plotly.js
docs/articles/data_processing_files/plotlyjs-1.29.2/LICENSE
docs/articles/data_processing_files/plotlyjs-1.29.2/plotly-htmlwidgets.css
docs/articles/data_processing_files/plotlyjs-1.29.2/plotly-latest.min.js
docs/articles/data_processing_files/typedarray-0.1/LICENSE
docs/articles/data_processing_files/typedarray-0.1/typedarray.min.js
docs/articles/flow.html
docs/articles/flow_files/DiagrammeR-binding-1.0.0/DiagrammeR.js
docs/articles/flow_files/DiagrammeR-styles-0.2/styles.css
docs/articles/flow_files/chromatography-0.1/LICENSE
docs/articles/flow_files/chromatography-0.1/chromatography.js
docs/articles/flow_files/d3-3.3.8/LICENSE
docs/articles/flow_files/d3-3.3.8/d3.min.js
docs/articles/flow_files/dagre-0.4.0/LICENSE
docs/articles/flow_files/dagre-0.4.0/dagre-d3.min.js
docs/articles/flow_files/font-awesome-4.5.0/css/font-awesome.css
docs/articles/flow_files/font-awesome-4.5.0/css/font-awesome.min.css
docs/articles/flow_files/font-awesome-4.5.0/fonts/fontawesome-webfont.ttf
docs/articles/flow_files/htmlwidgets-1.1/htmlwidgets.js
docs/articles/flow_files/mermaid-0.3.0/LICENSE
docs/articles/flow_files/mermaid-0.3.0/dist/mermaid.css
docs/articles/flow_files/mermaid-0.3.0/dist/mermaid.slim.min.js
docs/articles/index.html
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/index.html
docs/reference/tor_add_metadata.html
docs/reference/tor_add_protein_counts_info.html
docs/reference/tor_add_uniprot_info.html
docs/reference/tor_calculate_degradation_dissipation.html
docs/reference/tor_calculate_growth_params.html
docs/reference/tor_calculate_label_rate.html
docs/reference/tor_calculate_labeled_fraction.html
docs/reference/tor_fetch_kegg_details.html
docs/reference/tor_fetch_kegg_pathway_details.html
docs/reference/tor_fetch_kegg_pathway_maps.html
docs/reference/tor_fetch_kegg_pathways_for_species.html
docs/reference/tor_fetch_kegg_species.html
docs/reference/tor_fetch_uniprot_proteins.html
docs/reference/tor_fetch_uniprot_species.html
docs/reference/tor_filter_label_rate_fits.html
docs/reference/tor_filter_peptides_by_spectral_fit_quality.html
docs/reference/tor_plot_label_rate_error.html
docs/reference/tor_plot_label_rate_hist.html
docs/reference/tor_plot_labeling_curves.html
docs/reference/tor_read_protein_counts_data.html
docs/reference/tor_read_svm_data_file.html
docs/reference/tor_recode_protein_ids.html
docs/reference/tor_remove_list_columns.html
docs/reference/tor_show_package_structure.html
docs/reference/turnoveR-package.html
docs/sitemap.txt
man/tor_add_metadata.Rd
man/tor_add_protein_counts_info.Rd
man/tor_add_uniprot_info.Rd
man/tor_calculate_degradation_dissipation.Rd
man/tor_calculate_growth_params.Rd
man/tor_calculate_label_rate.Rd
man/tor_calculate_labeled_fraction.Rd
man/tor_fetch_kegg_details.Rd
man/tor_fetch_kegg_pathway_details.Rd
man/tor_fetch_kegg_pathway_maps.Rd
man/tor_fetch_kegg_pathways_for_species.Rd
man/tor_fetch_kegg_species.Rd
man/tor_fetch_uniprot_proteins.Rd
man/tor_fetch_uniprot_species.Rd
man/tor_filter_label_rate_fits.Rd
man/tor_filter_peptides_by_spectral_fit_quality.Rd
man/tor_plot_label_rate_error.Rd
man/tor_plot_label_rate_hist.Rd
man/tor_plot_labeling_curves.Rd
man/tor_read_protein_counts_data.Rd
man/tor_read_svm_data_file.Rd
man/tor_recode_protein_ids.Rd
man/tor_remove_list_columns.Rd
man/tor_show_package_structure.Rd
man/turnoveR-package.Rd
rename_prot.xlsx
test_scripts/Proteome_sectors_masterlist.csv
test_scripts/kegg_testing.Rmd
test_scripts/metadata.xlsx
test_scripts/metadata_CMW.xlsx
test_scripts/svm.Rmd
test_scripts/testing.Rmd
test_scripts/time_point_info_007.xlsx
test_scripts/time_point_info_035.xlsx
tests/testthat.R
tests/testthat/test-kegg.R
tests/testthat/test-svm-data.R
tests/testthat/test_data/psms.csv
tests/testthat/test_data/rename_prot.txt
tests/testthat/test_data/rename_prot.xlsx
tests/testthat/test_data/rename_prot_bad.xlsx
tests/testthat/test_data/svm_pred_results.csv
tests/testthat/test_data/svm_pred_results_0.03gr.csv
tests/testthat/test_data/svm_pred_results_bad.csv
tests/testthat/test_data/svm_pred_wt007_manualfilt.txt
tests/testthat/test_data/svm_pred_wt035_manualfilt.txt.txt
tests/testthat/test_protein_degradation.R
tests/testthat/test_visualization.R
turnoveR.Rproj
vignettes/data_processing.Rmd
vignettes/flow.Rmd
vignettes/vignette_data/metadata_CMW.xlsx
vignettes/vignette_data/psms.csv
vignettes/vignette_data/rename_prot.xlsx
vignettes/vignette_data/svm_pred_results_0.03gr.csv
vignettes/vignette_ideas.md
