Files in vivaldi
Viral Variant Location and Diversity
MD5
README.md
NAMESPACE
DESCRIPTION
LICENSE
R/merge_replicates.R
R/dNdS_segment.R
R/snv_genome.R
R/data.R
R/snv_location.R
R/filter_variants.R
R/shared_snv_plot.R
R/position_allele_freqs.R
R/snpeff_info.R
R/arrange_data.R
R/tstv_plot.R
R/prepare_annotations.R
R/add_metadata.R
R/read_reference_fasta_dna.R
R/tstv_ratio.R
R/plot_shannon.R
R/globals.R
R/af_distribution.R
R/snv_segment.R
R/shannon_entropy.R
R/shared_snv_table.R
R/tally_it.R
inst/CITATION
inst/doc/vignette.Rmd
inst/doc/vignette.R
inst/doc/vignette.html
inst/extdata/H1N1.fa
inst/extdata/reps.csv
inst/extdata/SegmentSize.csv
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a2_frac_0.01_BWA_ivar_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a3_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a1_frac_0.01_BWA_ivar_custom.ann.vcf
inst/extdata/vcfs/H1N1-random4_m2_AF_random-a4_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a3_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random4_m2_AF_random-a4_frac_0.01_BWA_ivar_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a2_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a3_frac_0.01_BWA_ivar_custom.ann.vcf
inst/extdata/vcfs/H1N1-random4_m1_AF_random-a4_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a1_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a1_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a1_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a3_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random4_m1_AF_random-a4_frac_0.01_BWA_ivar_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a2_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random4_m1_AF_random-a4_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random4_m2_AF_random-a4_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a3_frac_0.01_BWA_ivar_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a1_frac_0.01_BWA_ivar_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a3_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a2_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a1_frac_0.01_BWA_varscan_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m2_AF_random-a2_frac_0.01_BWA_freebayes_custom.ann.vcf
inst/extdata/vcfs/H1N1-random3_m1_AF_random-a2_frac_0.01_BWA_ivar_custom.ann.vcf
build/vignette.rds
tests/testthat.R
tests/testthat/test-snv_segment.R
tests/testthat/test-snv_location.R
tests/testthat/test-tally_it.R
tests/testthat/test-shared_snv_table.R
tests/testthat/test-position_allele_freqs.R
tests/testthat/test-tstv_ratio.R
tests/testthat/test-filter_variants.R
tests/testthat/test-tstv_plot.R
tests/testthat/test-shannon_entropy.R
tests/testthat/test-prepare_annotations.R
tests/testthat/test-shared_snv_plot.R
tests/testthat/test-af_distribution.R
tests/testthat/test-add_metadata.R
tests/testthat/test-snv_genome.R
tests/testthat/test-merge_replicates.R
vignettes/vignette.Rmd
data/example_filtered_SNV_df.rda
man/shared_snv_table.Rd
man/snv_segment.Rd
man/af_distribution.Rd
man/prepare_annotations.Rd
man/filter_variants.Rd
man/shared_snv_plot.Rd
man/shannon_entropy.Rd
man/plot_shannon.Rd
man/dNdS_segment.Rd
man/snpeff_info.Rd
man/read_reference_fasta_dna.Rd
man/tstv_plot.Rd
man/snv_genome.Rd
man/position_allele_freq.Rd
man/add_metadata.Rd
man/example_filtered_SNV_df.Rd
man/snv_location.Rd
man/arrange_data.Rd
man/merge_replicates.Rd
man/tstv_ratio.Rd
man/tally_it.Rd
