673757f8308194ab2ae2fa9280036493 *DESCRIPTION
0fffce9ec60ee30dda9a01200ab6045d *LICENSE
b60cf5725a1df52561c430a08ac15f91 *NAMESPACE
28e21cf3ecfd85f938b8e5bc0305aaa3 *R/add_metadata.R
0aa92d10ed9dd8d1b5e6f0070954c982 *R/af_distribution.R
12ddc074e5ce18cd966dc38abf3c0af7 *R/arrange_data.R
2f6e7e41b1163ae0b45ea6868841e040 *R/dNdS_segment.R
f36b13b7acba5530321877fb910d5b3e *R/data.R
0cf0f0a73cc29942fd16afa4f8bc5381 *R/filter_variants.R
06c3720750556bb1003afb949eb76bc0 *R/globals.R
547edd97aa0910ae53ccfdd5449e0985 *R/merge_replicates.R
9f2774f3d30a8a4816e870de9f44db5d *R/plot_shannon.R
2164854e71464e260bce0c874af070c2 *R/position_allele_freqs.R
dca330845ac5df9a674979652f2113fa *R/prepare_annotations.R
99f09fd60b9266f7e9ad87a278907677 *R/read_reference_fasta_dna.R
f5b59174d978c73ed32fb9751935c3af *R/shannon_entropy.R
6398459c42e5845b81d258c525d41d01 *R/shared_snv_plot.R
b33cdf5faece8abc25b619ac9e580fcc *R/shared_snv_table.R
ea26450cffa806a5f3671be984f6b8a8 *R/snpeff_info.R
0ee8541537d5b1b06f178fcd568013d2 *R/snv_genome.R
53d454f276adc0cf4496048e02b1d79a *R/snv_location.R
1b65c9cba0aa2a1907ba693c674b5a04 *R/snv_segment.R
750c7ba5dd54cfbee7187b913651867b *R/tally_it.R
e102ccc85e83bdf32b7662f297324d50 *R/tstv_plot.R
3690db5afa1664852c6a881c88b8bfa4 *R/tstv_ratio.R
7699c9be880b88a34980727f0043bb60 *README.md
7bcc3906e04496c16012d084983ef1d3 *build/vignette.rds
c2ddb481dcde797d5919a4d428226e9c *data/example_filtered_SNV_df.rda
fb0bed86ff9cc26bb2c4152a35264f67 *inst/CITATION
21a584414e72d096da45046b3df7d90f *inst/doc/vignette.R
be1709f04a451b41abce5326343a6cc2 *inst/doc/vignette.Rmd
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9b77aaf6c176f4c48b07c0f8d53ffcc9 *inst/extdata/H1N1.fa
46007f40c6dda9c5db444c7f0f7dfd3d *inst/extdata/SegmentSize.csv
7d35bc671bc434edbb015a99b88ac0cb *inst/extdata/reps.csv
ce975938494fb7df8300302c55dda72c *inst/extdata/vcfs/H1N1-random3_m1_AF_random-a1_frac_0.01_BWA_freebayes_custom.ann.vcf
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bc90739fd2035a52732e7f92dd17c5b3 *inst/extdata/vcfs/H1N1-random3_m2_AF_random-a2_frac_0.01_BWA_varscan_custom.ann.vcf
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db1430696beb4b6e9647af2d5131ca2e *inst/extdata/vcfs/H1N1-random3_m2_AF_random-a3_frac_0.01_BWA_ivar_custom.ann.vcf
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f837726954242cc709c13a5594f03bab *man/add_metadata.Rd
44903196f714c8a51e2efc4743c4ee06 *man/af_distribution.Rd
95c0be3f65d17daf559924bc6a2ceabe *man/arrange_data.Rd
c7b812c7fe36dac6a0b480bd9668cd05 *man/dNdS_segment.Rd
a751bc4ee91cd9526c875840b8b3dede *man/example_filtered_SNV_df.Rd
67a6daab5723bc1e7afd7c7348ff1e7a *man/filter_variants.Rd
7ca0a8a3c3828134a1c742b37753734e *man/merge_replicates.Rd
2786c653717ddc441a661ae0aca1ae3b *man/plot_shannon.Rd
2304ad771aedf4ac72c6d272914352e9 *man/position_allele_freq.Rd
0d076854a71a286c3c226a995ae0161f *man/prepare_annotations.Rd
63ea4c7c70f4800efca96131870eef8a *man/read_reference_fasta_dna.Rd
cbc15ef6d84d3bdcaeca41bce1f20865 *man/shannon_entropy.Rd
9a86c9e55274f8915715d9ec494df4e9 *man/shared_snv_plot.Rd
18a56216c36f4ed2315ad007bcb17732 *man/shared_snv_table.Rd
2b6e6da40fa249054c62d21946714fd4 *man/snpeff_info.Rd
6581ebf166081ca158bdad3b7a795454 *man/snv_genome.Rd
775de4c21946caad82868e3fd53942da *man/snv_location.Rd
d52313261b84d4e6ccb221d46cb5a7db *man/snv_segment.Rd
4f0e270199ae43071c5096dfeb8ea382 *man/tally_it.Rd
fd4dfff75841b44ee9d406fa6d3fe5b3 *man/tstv_plot.Rd
cc8f764b8c1b641148680ce996e70f45 *man/tstv_ratio.Rd
2f922ff899c968c4d55b5010a533a6ed *tests/testthat.R
e109d8b66b4209bd0bfb77c1a0769484 *tests/testthat/test-add_metadata.R
dd2741e94adea107d1c04cc7d2f909ce *tests/testthat/test-af_distribution.R
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5be558de0deee5fa52aa3459c226b201 *tests/testthat/test-merge_replicates.R
5418d6384b5254b806efdb5c1b2b0921 *tests/testthat/test-position_allele_freqs.R
4a978a07bffaae79be0514266a628dda *tests/testthat/test-prepare_annotations.R
1b7bef356e934ba895bb0bb39e6f3b6e *tests/testthat/test-shannon_entropy.R
429cc3a10f228e96d908487853328838 *tests/testthat/test-shared_snv_plot.R
6a1881dab876eccd52ce4af08c06ca2f *tests/testthat/test-shared_snv_table.R
d08d44f77267c817608239f8b2406180 *tests/testthat/test-snv_genome.R
b5b7e846f5becc9982c54dab50d5b421 *tests/testthat/test-snv_location.R
6ce84571c73bf4e7af55ba8740c69f42 *tests/testthat/test-snv_segment.R
4721da968e02766eb62cf090a7ac3f13 *tests/testthat/test-tally_it.R
f5c6280426fa0f5a44ea0a8546eb3da4 *tests/testthat/test-tstv_plot.R
348ad3e4b47b46c7605773890c69ec74 *tests/testthat/test-tstv_ratio.R
be1709f04a451b41abce5326343a6cc2 *vignettes/vignette.Rmd
