ca54a5762bae371d2025654720e9d3c3 *DESCRIPTION
89388ad897aa044a6dd88dffe8ba893f *INSTALL
7045494deddc5c366bc486016579a04c *NAMESPACE
ea197a2f3a1f0e085e6eef9111ce1e2a *NEWS.md
8107912446641c899b1862bce5fd607d *R/apply_bcftools_norm.R
e13519b4dd03f81c43cd0e83423cdb68 *R/check_if_ref_matches_fasta.R
4cd37743e6e2a7eedf9e5edae47c1f34 *R/check_parameters.R
09a5ad9f26edc9620282c581c0879e04 *R/compare_read_to_ref_wt_and_mut.R
40855509f957553373ac9b8e9849f8ec *R/extract_fragment_features.R
867c4702345639c812607fdf95087107 *R/fRagmentomics-package.R
1c618193fcb945107786e2b2b6702842 *R/get_base_basq_mstat_from_read.R
013d0635c776d149e4982afb20cf07b7 *R/get_fragment_bases_5p_3p.R
fbee4cc3cbf769f239bcb5dedcd9bb1b *R/get_fragment_bases_5p_3p_softclip.R
fd6e224a3a6e7c5fda536b5aaa2b6b50 *R/get_fragment_size.R
dbb06a241ba4d32af2f89d9456c2c3cf *R/get_index_aligning_with_pos.R
f7057b2e97bdb9cdbabfe119d60be65d *R/get_mutation_status_of_fragment.R
efd452726ead3f67e5c50d7c3dba9529 *R/get_mutation_status_of_read.R
810bef62b4b66f24440237090a58b801 *R/globals.R
feaea7f7135acb3b101f0a7d5d17cf0c *R/normalize_mut.R
74358385e8a834875931643d42a63e73 *R/normalize_to_vcf_rep.R
a461a3c564995f04f1d42f9449895f03 *R/plot_freq_barplot.R
0b7e6417d60f7fd0d6f9c8595a280571 *R/plot_motif_barplot.R
5541babc90263d66c965880e118a4678 *R/plot_motif_ggseqlogo.R
fddaf466a6771f8ca4c12e3f32c090f8 *R/plot_size_distribution.R
e158453911f2614a1498ef508ad61b76 *R/process_fragment_reads_QC.R
ef28131fb53aec9e12e889c784ca0b58 *R/read_bam.R
6b364796b5842f6236fbcd412cf697bf *R/read_mut.R
1d9181fa1d3186275e7e97f22415a709 *R/remove_bad_mut.R
f0fe87e08ef55f382faca9f08e0f1d83 *R/remove_softclip.R
cc3aa3131a70e23b8d6452dce9125a01 *R/run_fRagmentomics.R
35f0459b516d8e5e62c917c5f8d76102 *R/search_for_indel_in_cigar.R
8407ca492540e7514c31cf1bc4134014 *R/utils.R
11823f8c5edfa00f2935e0907328783d *R/utils_fasta.R
b66660ddbc2de2dc09b95a2f7005752d *README.md
1e02d610fa90bf407f4d7068a8580df1 *build/vignette.rds
453ac80c12cbbf461dd87544c98f6dd2 *inst/doc/fRagmentomics.R
767089ef137412b40476d134b7912e0e *inst/doc/fRagmentomics.Rmd
d93b047194fb32dfdc9106adc882aeeb *inst/doc/fRagmentomics.html
3e12e06640c8fd2a09adb8d8e9cafc5b *inst/extdata/bam/cfdna-egfr-del_chr7_55241864_55243064_10k.bam
58ed18afb0bb7763dae1911b65d3a101 *inst/extdata/bam/cfdna-egfr-del_chr7_55241864_55243064_10k.bam.bai
c7210ba4958d8169697d6549a5f1f7e3 *inst/extdata/fasta/hg19_chr7_55231864_55253064.fa
9f6f958204a17f1071d0d81ffe3fb8a0 *inst/extdata/fasta/hg19_chr7_55231864_55253064.fa.fai
99fa4f83903c1067525cd730bb93405f *inst/extdata/mutation/cfdna-egfr-del_chr7_55241864_55243064_10k.mutations.tsv
90875bfd6d9ef611ab74825147b6c84f *inst/scripts/anonymize_snps.py
ba01b4cd8bf065a253d2cedce68e7544 *inst/scripts/anonymize_snps.sh
e7eda79df459837be3fa8eb8323a9fd9 *inst/scripts/run.sh
aee46501bf7c8d25c8b5c8bd1e0cca67 *inst/scripts/subsample_and_anonymize_reads.sh
38644ce251ed19c48d810ee98b46c276 *man/apply_bcftools_norm.Rd
e6d91132fe886df8ce9ae5437588f21f *man/check_bcftools_is_installed.Rd
0f317fd3daa50385505e8abc6a0d36f8 *man/check_parameters.Rd
875b11b161d83fd02e8328742389b60a *man/compare_read_to_ref_wt_and_mut.Rd
475f953e410213915c3dd139ca4ae2fe *man/extract_fragment_features.Rd
3cad7de1144d2117d3eb05a9b6351e51 *man/fRagmentomics-package.Rd
17e6db724c061c16c5fa40a2aa81c6bd *man/figure/Fragment_Size_fRagmentomics.png
82d0f8c42abe6cd9e439b49e1ccd6cd3 *man/figure/Fragment_Status_fRagmentomics.png
7a7069405c61ecb5126fd8664fc54768 *man/figure/Workflow_fRagmentomics.png
9899722443e09f687f6ced89914be9e8 *man/figure/complete_application_example_EGFR.png
0b18626f063c07ab57093cad166d4fab *man/figure/logo.svg
8f705b5315e2752a7daa1e3160b20b8b *man/figure/plot_README_freq_barplot.png
5f23eb56b6959f24767196eacf09e558 *man/figure/plot_README_freq_barplot_differential.png
025cba3930f1605a0d8226c31c3d92fc *man/figure/plot_README_freq_barplot_splitbymotif.png
91728831d67f12253eb09dd49f03f6cb *man/figure/plot_README_ggseqlogo.png
49f0e96ea43864a8801a7dcbc7604efb *man/figure/plot_README_motif_barplot_splitbybase.png
d164ad50e166dfcf9748da71f34d35e1 *man/figure/plot_README_size_distribution.png
4222166e79769c05138e469f44493921 *man/figure/size_compared_to_ref_genome_1.png
de2fb5c196cbbc973560e0202e675d0d *man/figure/size_compared_to_ref_genome_2.png
f74f18594ddb2f2c54f43bb268819c38 *man/get_base_basq_from_read_at_pos.Rd
26c8ac4712803c5b0b3765b05a9d9700 *man/get_base_basq_mstat_from_read.Rd
75d4fcac34e5257f074dddfbeb079393 *man/get_fragment_bases_5p_3p.Rd
8b998346b64fff41001d70fa621494ca *man/get_fragment_bases_5p_3p_softclip.Rd
254a42eadb155974b4ad94894ab078d6 *man/get_fragment_size.Rd
4c55c5e71420071fcf2c9abae6468988 *man/get_index_aligning_with_pos.Rd
9ab1b0d76ad43e9a1cad52febe72083b *man/get_mutation_status_of_fragment.Rd
a65187df585e1c49787e3b3ed720487d *man/get_mutation_status_of_read.Rd
502b156acb23e5e423f30254bf6ae2ca *man/get_number_of_common_first_char.Rd
ceca13fb79a8016b5367fe30fc228ea3 *man/normalize_mut.Rd
a0cc8a61ba721fe11ce22d6f325c5029 *man/normalize_to_vcf_rep.Rd
887ec00398039f1a7e04e8e1ca368cbb *man/plot_freq_barplot.Rd
fec7b70907653c3b71e6325cb2ad93c1 *man/plot_ggseqlogo_meme.Rd
494bcee29591b2cfa9acd3095baf0178 *man/plot_motif_barplot.Rd
7f625e419172e1cc1f8f5d273846f0a5 *man/plot_size_distribution.Rd
22a18cb08dbe41382ff8b2ead8e97980 *man/read_bam.Rd
ba3bec85d236bdf1ac136af62aa0b323 *man/read_mut.Rd
ce91392b7b2d9fcba336c9fa6f8aa635 *man/remove_bad_mut.Rd
b70c819dc7c205a13e29bb2f343edd95 *man/run_fRagmentomics.Rd
07e20e67994ef6791d4ee4de7f099228 *man/search_for_indel_in_cigar.Rd
a2c795b48a73b1b52c51452380e17519 *tests/testthat.R
11dd87b6885ba5efd7ce06aee0ab7b57 *tests/testthat/helper-functions.R
4549cfcf7625271bcd6ac84021ee2838 *tests/testthat/test-apply_bcftools_norm.R
06305f8b4992adc45fb9de690c265b64 *tests/testthat/test-check_parameters.R
27136adfb75edab7ed2e91f4803a9911 *tests/testthat/test-extract_fragment_features.R
53e62f945145de22d7f511e4ae4fecc4 *tests/testthat/test-get_base_basq_mstat_from_read.R
a01035502e1aabd9ad048d79dd97b807 *tests/testthat/test-get_fragment_bases_5p_3p.R
60ddc7348150a710a6350180f9b5ca22 *tests/testthat/test-get_fragment_bases_5p_3p_softclip.R
0ecd7a5a010d3858ae4dec3a582c7d06 *tests/testthat/test-get_fragment_size.R
ab6eda894cd20d6f80654573e6fa1350 *tests/testthat/test-get_mutation_status_of_fragment.R
38a912579cc9c8dc8bdda48c8372c598 *tests/testthat/test-get_mutation_status_of_read.R
a3a7b567a5a4f7315ef7c25c01aadb53 *tests/testthat/test-normalize_to_vcf_rep.R
bffc128cc68e3ea85b3f8c9112bf02e2 *tests/testthat/test-plot_freq_barplot.R
847a5850e55fd2af48a340f093d63a1c *tests/testthat/test-plot_motif_barplot.R
0c3cf17323a71d6040ffee402b14c36e *tests/testthat/test-plot_motif_ggseqlogo.R
075d0ec80a6395a458e250896cfa9798 *tests/testthat/test-plot_size_distribution.R
00b31a1acab21ae620f5137b179e1999 *tests/testthat/test-process_fragment_reads_qc.R
38ff7c2e4d2a1333a924496a93b76543 *tests/testthat/test-read_bam.R
1e174c4b912c10824db602a8e4b66364 *tests/testthat/test-read_mut.R
e1f870d476acd38a7230f0283c56254a *tests/testthat/test-remove_bad_mut.R
e122e3983ddac848b3b8afa8d2a842a4 *tests/testthat/test-remove_softclip.R
66a148393322f9dfb94de642ec94fe0b *tests/testthat/test-run_fRagmentomics.R
0722fa274ad9fb4ec078380b479f2df3 *tests/testthat/test-search_for_indel_in_cigar.R
495946b2d407000fa3f7a61c33a23e42 *tests/testthat/test-utils.R
d02f8c51329811236770d4e42a774e27 *tests/testthat/test-utils_fasta.R
767089ef137412b40476d134b7912e0e *vignettes/fRagmentomics.Rmd
