Files in jeffkimbrel/MappgeneSummary
Summarize Mappgene SNV Data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
MappgeneSummary.Rproj
NAMESPACE
NOTICE
R/add_SNV.R
R/add_zika_reference.R
R/copy_summary_template.R
R/data.R
R/diversity.R
R/get_coverages.R
R/get_mappgene_data.R
R/get_outbreak_dates.R
R/get_outbreak_info.R
R/make_venn.R
R/plot_effect_counts.R
R/plot_heatmap.R
R/plot_nmds.R
R/plot_outbreak_info.R
R/ref_alt.R
README.md
data-raw/examples.R
data-raw/zika_reference.R
data/example_df_A_ivar.rda
data/example_df_A_lofreq.rda
data/example_df_B_ivar.rda
data/example_df_B_lofreq.rda
data/example_df_C_ivar.rda
data/example_df_C_lofreq.rda
data/zika_genes.rda
data/zika_reference.rda
initialize.R
inst/extdata/NC_045512.2.fasta
inst/extdata/NC_045512.2.gbk.ffn
inst/extdata/mutation list for VOC and VOI 11.16.21.xlsx
inst/extdata/mutation list for VOC and VOI 12.02.21v2.xlsx
inst/extdata/updated omicron and sublineages mutations 05.04.2022.xlsx
inst/extdata/zika_KJ776791.xlsx
inst/python/entropycalculator.py
inst/python/mappygene.py
inst/rmd/style.css
inst/rmd/summary_template.Rmd
inst/test_files/sampleA.ivar.lofreq.snpSIFT.txt
inst/test_files/sampleA.ivar.snpSIFT.txt
inst/test_files/sampleB.ivar.lofreq.snpSIFT.txt
inst/test_files/sampleB.ivar.snpSIFT.txt
inst/test_files/sampleC.ivar.lofreq.snpSIFT.txt
inst/test_files/sampleC.ivar.snpSIFT.txt
man/add_SNV.Rd
man/add_zika_reference.Rd
man/copy_summary_template.Rd
man/example_df_A_ivar.Rd
man/example_df_A_lofreq.Rd
man/example_df_B_ivar.Rd
man/example_df_B_lofreq.Rd
man/example_df_C_ivar.Rd
man/example_df_C_lofreq.Rd
man/get_country_outbreak_info.Rd
man/get_coverages.Rd
man/get_global_outbreak_info.Rd
man/get_outbreak_info.Rd
man/get_outbreak_latest.Rd
man/get_outbreak_peak.Rd
man/get_outbreak_start.Rd
man/get_state_outbreak_info.Rd
man/gini_simpson.Rd
man/hill_12I.Rd
man/make_venn.Rd
man/parse_ref_alt.Rd
man/plot_coverage_ecdf.Rd
man/plot_effect_counts.Rd
man/plot_heatmap.Rd
man/plot_nmds.Rd
man/plot_outbreak_milestones.Rd
man/plot_outbreak_trends.Rd
man/read_mappgene_data.Rd
man/simpson.Rd
man/view_HGVS_C.Rd
man/zika_reference.Rd
vignettes/.gitignore
vignettes/my-vignette.Rmd
