Files in gian-asco/test
Longitudinal Analysis of Cancer Evolution (LACE)
.Rbuildignore
.github/.gitignore
.github/workflows/check-development.yml
.github/workflows/check-master.yml
.gitignore
DESCRIPTION
LACE2integ.Rproj
LICENSE
NAMESPACE
R/LACEinterface.R
R/LACEview2.R
R/data.R
R/frontend.R
R/inference.R
R/timescape.R
R/utils.R
R/visualization.R
README.md
_pkgdown.yml
data/inference.RData
data/longitudinal_sc_variants.RData
inst/CITATION
inst/NEWS.Rd
inst/htmlwidgets/LACE.js
inst/htmlwidgets/LACE.yaml
inst/htmlwidgets/lib/bootstrap.min.css
inst/htmlwidgets/lib/bootstrap.min.js
inst/htmlwidgets/lib/colorbrewer.js
inst/htmlwidgets/lib/cytoscape-cxtmenu.js
inst/htmlwidgets/lib/cytoscape-dagre.js
inst/htmlwidgets/lib/cytoscape-popper.js
inst/htmlwidgets/lib/cytoscape.min.js
inst/htmlwidgets/lib/d3-color.min.js
inst/htmlwidgets/lib/d3-interpolate.min.js
inst/htmlwidgets/lib/d3-scale-chromatic.v1.min.js
inst/htmlwidgets/lib/d3.min.js
inst/htmlwidgets/lib/d3.tip.v0.6.3.js
inst/htmlwidgets/lib/d3.v4.js
inst/htmlwidgets/lib/dagre.min.js
inst/htmlwidgets/lib/jquery-2.1.4.js
inst/htmlwidgets/lib/jquery.dataTables.min.css
inst/htmlwidgets/lib/jquery.dataTables.min.js
inst/htmlwidgets/lib/jquery.layout.min.js
inst/htmlwidgets/lib/jquery.min.js
inst/htmlwidgets/lib/my_svg_crowbar.js
inst/htmlwidgets/lib/popper.js
inst/htmlwidgets/lib/run_timescape.js
inst/htmlwidgets/lib/timescape.css
inst/htmlwidgets/lib/timesweep.css
inst/htmlwidgets/lib/tippy.css
inst/htmlwidgets/lib/tippy.js
inst/htmlwidgets/lib/underscore.js
inst/htmlwidgets/lib/vanilla-dataTables.min.css
inst/htmlwidgets/lib/vanilla-dataTables.min.js
inst/shinyapp/Rambow_dataset/config/.config_01_m.yml
inst/shinyapp/Rambow_dataset/config/.config_02_av.yml
inst/shinyapp/Rambow_dataset/config/.config_03_thr.yml
inst/shinyapp/Rambow_dataset/config/.config_04_dp.yml
inst/shinyapp/Rambow_dataset/config/.config_05_va.yml
inst/shinyapp/Rambow_dataset/config/.config_06_inf.yml
inst/shinyapp/Rambow_dataset/data_info.rds
inst/shinyapp/Rambow_dataset/filtered_var/D.RData
inst/shinyapp/Rambow_dataset/filtered_var/snpMut_filt_freq_reduced.txt
inst/shinyapp/Rambow_dataset/filtered_var/valid_distinct_mutations.RData
inst/shinyapp/Rambow_dataset/filtered_vcf/SNPInfo.rds
inst/shinyapp/Rambow_dataset/filtered_vcf/cells_aggregate_info.rds
inst/shinyapp/Rambow_dataset/filtered_vcf/scMutInfo.rds
inst/shinyapp/Rambow_dataset/filtered_vcf/snpMut_filt.rds
inst/shinyapp/Rambow_dataset/filtered_vcf/snpMut_filt_freq.rds
inst/shinyapp/Rambow_dataset/inference.RData
inst/shinyapp/Rambow_dataset/sam_out/final_data_depth.txt
inst/shinyapp/Rambow_dataset/sam_out/final_data_mut.txt
inst/shinyapp/Small_dataset/config/.config_01_m.yml
inst/shinyapp/Small_dataset/config/.config_02_av.yml
inst/shinyapp/Small_dataset/config/.config_03_thr.yml
inst/shinyapp/Small_dataset/config/.config_04_dp.yml
inst/shinyapp/Small_dataset/config/.config_05_va.yml
inst/shinyapp/Small_dataset/config/.config_06_inf.yml
inst/shinyapp/Small_dataset/config/config_01_m.yml
inst/shinyapp/Small_dataset/config/config_02_av.yml
inst/shinyapp/Small_dataset/config/config_03_thr.yml
inst/shinyapp/Small_dataset/config/config_04_dp.yml
inst/shinyapp/Small_dataset/config/config_05_va.yml
inst/shinyapp/Small_dataset/config/config_06_inf.yml
inst/shinyapp/Small_dataset/data_info.rds
inst/shinyapp/Small_dataset/filtered_var/D.RData
inst/shinyapp/Small_dataset/filtered_var/snpMut_filt_freq_reduced.txt
inst/shinyapp/Small_dataset/filtered_var/valid_distinct_mutations.RData
inst/shinyapp/Small_dataset/filtered_vcf/SNPInfo.rds
inst/shinyapp/Small_dataset/filtered_vcf/cells_aggregate_info.rds
inst/shinyapp/Small_dataset/filtered_vcf/scMutInfo.rds
inst/shinyapp/Small_dataset/filtered_vcf/snpMut_filt.rds
inst/shinyapp/Small_dataset/filtered_vcf/snpMut_filt_freq.rds
inst/shinyapp/Small_dataset/inference.RData
inst/shinyapp/Small_dataset/sam_out/final_data_depth.txt
inst/shinyapp/Small_dataset/sam_out/final_data_mut.txt
inst/shinyapp/Small_dataset/vcf_out/SRR7424152.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424152.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424152.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424152.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424153.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424153.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424153.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424153.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424154.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424154.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424154.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424154.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424339.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424339.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424339.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424339.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424340.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424340.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424340.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424340.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424341.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424341.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424341.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424341.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424479.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424479.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424479.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424479.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424480.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424480.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424480.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424480.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424481.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424481.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424481.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424481.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424713.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424713.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424713.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424713.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424714.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424714.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424714.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424714.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424715.filtered.anninput
inst/shinyapp/Small_dataset/vcf_out/SRR7424715.filtered.anninput.exonic_variant_function
inst/shinyapp/Small_dataset/vcf_out/SRR7424715.filtered.anninput.log
inst/shinyapp/Small_dataset/vcf_out/SRR7424715.filtered.anninput.variant_function
inst/shinyapp/Small_dataset/vcf_out/stderr.log
inst/shinyapp/Small_dataset/vcf_out/stdout.log
inst/shinyapp/alpha_beta_table.R
inst/shinyapp/annotation.R
inst/shinyapp/app.R
inst/shinyapp/depth_computation.R
inst/shinyapp/filters_computation.R
inst/shinyapp/inference_tab.R
inst/shinyapp/info_help.R
inst/shinyapp/install
inst/shinyapp/load_and_save.R
inst/shinyapp/make_lace_final_input.R
inst/shinyapp/pipeline_io_ctrl.R
inst/shinyapp/project_mgr.R
inst/shinyapp/project_tab.R
inst/shinyapp/step3_explore_lace_input_data.R
man/LACE.Rd
man/LACE2.Rd
man/compute.mutation.distance.Rd
man/compute.variants.error.rates.Rd
man/inference.Rd
man/lace_interface.Rd
man/longitudinal.tree.plot.Rd
man/longitudinal_sc_variants.Rd
tests/testthat.R
tests/testthat/test_algorithm.R
vignettes/1_introduction.Rmd
vignettes/2_running_LACE.Rmd
vignettes/3_LACE_interface.Rmd
vignettes/LACE1.Rnw
vignettes/LACE2.Rnw
vignettes/resources/Annotation_tab.png
vignettes/resources/Depth_tab.png
vignettes/resources/Display_tab.png
vignettes/resources/Filters_tab.png
vignettes/resources/Inference_tab1.png
vignettes/resources/Inference_tab2.png
vignettes/resources/Interactive_Variant_tab.png
vignettes/resources/Interactive_Variant_tab2.png
vignettes/resources/Project_tab.png
vignettes/resources/Projects_menu.png
vignettes/resources/SCmeta_tab.png
vignettes/resources/Variant_tab.png
vignettes/resources/load_project.png
vignettes/resources/pd.cfg
vignettes/resources/samples_order.png
vignettes/resources/select_variant.png
