413a9ba4d811a196d7584a09bce8f27f *DESCRIPTION
e52c73a9e29e3578940a254b0c960c2e *NAMESPACE
1d71fe4ad0962ff727c96f5db43dcf33 *R/AlignmentsExperimentSet-class.R
c7b9a3740dfbae0076b04e4d9ec2ff72 *R/RcppExports.R
31d85e75218f13502a8ed55fdaa58d1f *R/amplican.R
f440e610dccfb72c60609d6ade267e45 *R/amplicanAlign.R
cf75d469c509d96df52cd5caea8b92db *R/amplicanFilter.R
414bca05a12323570aaad5ae0cc1aa2c *R/amplicanNormalize.R
ed4e95770a4bd9805d74144fa701605f *R/amplicanReport.R
dc870bc87063d41b1806cc73bd3ac08b *R/amplicanSummarize.R
d4a584ea87e8886804a2b7985276cc49 *R/ggforce_bezier.R
5ee2eead34dbcefcc881a4ec9372be11 *R/helpers_alignment.R
2399b90ff3d628568bf235e84e789fe5 *R/helpers_directory.R
073e29ece071b807074b59343f087a75 *R/helpers_filters.R
06b3d0247bb9b7bc3c3bc71b657b55f9 *R/helpers_general.R
9b7270af20c48ca7de9b244c35f06be6 *R/helpers_plots.R
217fa2262acd9bfee7c9fda128d8c470 *R/helpers_rmd.R
7b76069c4fd6dd6db1f0d83c2e282337 *R/helpers_warnings.R
453045ae1335c6b3437a69ad4f5cae7c *README.md
5331f075481d6ad05cd9efb90abb7a04 *build/vignette.rds
e04a04da596bd025e6c0230ed1fcdb6f *inst/CITATION
a73def78df278b80f8975ff20e6a7e7d *inst/NEWS
ca5863169eefef09e5cb3e4889ba3200 *inst/TODO
22c1153df9da5aa066349a91dc711272 *inst/doc/amplicanFAQ.Rmd
1e13418c74de75535679dabf345614d2 *inst/doc/amplicanFAQ.html
371c4b6902ae45c17b3d71366eab2a9d *inst/doc/amplicanOverview.R
9c058f3451b48b21c910902bd51abcdd *inst/doc/amplicanOverview.Rmd
258b7842ca60d1b0e379a980981e2a92 *inst/doc/amplicanOverview.html
d54881254128e0bb00acba2c7234effa *inst/doc/example_amplicon_report.R
3fd3b92ac65ce84ec1cdcd21533a77c8 *inst/doc/example_amplicon_report.Rmd
54dac02cff20e073c2719a33393bbcb5 *inst/doc/example_amplicon_report.html
71661cecf910eca11a99d1807f2169cf *inst/doc/example_barcode_report.R
676b4ae6b2cb7d23445352a050a17417 *inst/doc/example_barcode_report.Rmd
07dc9966dec6d4ab9b979375cc4f5126 *inst/doc/example_barcode_report.html
5c33892ad98de51b99862d3febd68b49 *inst/doc/example_group_report.R
aba57432a7223a5da60656dbb1ea627a *inst/doc/example_group_report.Rmd
47e1ed89b4676938a24b388051262e6f *inst/doc/example_group_report.html
6d3962766beadbdb5487ab7516aa142e *inst/doc/example_guide_report.R
0c21776dd3b473f272ffe532821a7f3b *inst/doc/example_guide_report.Rmd
16f9cc3373b0a0513b71198cdabd0648 *inst/doc/example_guide_report.html
77bba944e15e4ee9ce444a1718e89b95 *inst/doc/example_id_report.R
0c8cd614c82f4c62c1f259fb3363120f *inst/doc/example_id_report.Rmd
89c15408980ccf2ca38bf495085e55f9 *inst/doc/example_id_report.html
eba431ac16188f8478b99d79635467d4 *inst/doc/example_index.R
657b7352c13fe03e8c933edeef3fcb3b *inst/doc/example_index.Rmd
6ca7d05e411c4651e54eee800bd36366 *inst/doc/example_index.html
76d9b86f9c262152ff6206ed59d5bfc9 *inst/extdata/R1_001.fastq
f031f958c70a89dd14ec295d2116f175 *inst/extdata/R1_002.fastq
d07236649c07ec61d4eec9914cc11833 *inst/extdata/R2_001.fastq
ce8dccc37a47aeaf8db8bdb912e601a9 *inst/extdata/R2_002.fastq
401443ce562868c24a7d23e749ab639a *inst/extdata/config.csv
593f00845f4a0b72084c1f7fc2d978fe *inst/extdata/results/RunParameters.txt
0c25fd11242e47df92fe8a61e667ef7c *inst/extdata/results/alignments/AlignmentsExperimentSet.rds
e7e905f9b9b7e34bd78684f2b20f3841 *inst/extdata/results/alignments/events_filtered_shifted.csv
e7e905f9b9b7e34bd78684f2b20f3841 *inst/extdata/results/alignments/events_filtered_shifted_normalized.csv
8df13d383cde6572eb65c20d9f8d7444 *inst/extdata/results/alignments/raw_events.csv
517d87c44263f7bba85d2900ed4c8f81 *inst/extdata/results/alignments/unassigned_reads.csv
273cf47bc407bb190e65968cf96d19a8 *inst/extdata/results/barcode_reads_filters.csv
6aaf85790c241a6c38b62b21ea911548 *inst/extdata/results/config_summary.csv
a8b8d1c7777cc4754d5964fff6afb862 *inst/rmarkdown/templates/amplicon_report/skeleton/skeleton.Rmd
655218255ebe76ff75d364fa460699ff *inst/rmarkdown/templates/amplicon_report/template.yaml
3f2768e7c166f07dfe1c2ecea9bef6ff *inst/rmarkdown/templates/barcode_report/skeleton/skeleton.Rmd
91dcd8aab8a92b0b874855a7fef5c4d8 *inst/rmarkdown/templates/barcode_report/template.yaml
f6af9ffcf1eb5c7c06097075d7f96af6 *inst/rmarkdown/templates/group_report/skeleton/skeleton.Rmd
d09ec79227254463515c1460602e23ea *inst/rmarkdown/templates/group_report/template.yaml
bb7067d3fd5088c30684e5b773612852 *inst/rmarkdown/templates/guide_report/skeleton/skeleton.Rmd
4f2ab0b3739252a8431f9d2ef5d04276 *inst/rmarkdown/templates/guide_report/template.yaml
31a40ae55946b82ed19a6fea8156fbdf *inst/rmarkdown/templates/id_report/skeleton/skeleton.Rmd
d0f78fe1028bf29d03ad956315e83e92 *inst/rmarkdown/templates/id_report/template.yaml
82ab89e1fea64a746fc780e39a12ddfb *inst/rmarkdown/templates/index_report/skeleton/skeleton.Rmd
08df645e81995db2d228de09f69a0cea *inst/rmarkdown/templates/index_report/template.yaml
60b0f0e1f1870a8c9e5ca15743d862ed *inst/test_data/test_aln.csv
08c09237fc07e51e8e66072379825ace *inst/test_data/test_cfg.csv
d514410b35cfec7b956d674775532697 *man/AlignmentsExperimentSet-class.Rd
b3f984c247cfb093e493bb9abdea88b6 *man/alphabetQuality.Rd
6877ea162750485c06b1271e40e4a999 *man/amplican.Rd
df6edef249c3076440e193956e166ea5 *man/amplicanAlign.Rd
b26d8f41a7cc37ee136620a0dd06cd1a *man/amplicanConsensus.Rd
4436e9bba298ea7e6bfecd977f671378 *man/amplicanFilter.Rd
834c99eff72f11852ae06404905c631d *man/amplicanMap.Rd
5207fedf2d1bfe008c39105edbc6c5e2 *man/amplicanNormalize.Rd
900b3ecf18cc018695f482decd90867b *man/amplicanOverlap.Rd
44eb918042ff9642825b80d558725c53 *man/amplicanPipeline.Rd
15e2e2e613556ac0adde521a7388356d *man/amplicanPipelineConservative.Rd
7e256811da3768a7f9161b65a1a94106 *man/amplicanReport.Rd
d61ada5c443473bd458f041e452b549f *man/amplicanSummarize.Rd
486d926a668a28c1472747e635eddbb8 *man/amplican_print_reads.Rd
b6096788e7725edd63b9cf1e9d9ec78b *man/assignedCount.Rd
d78ae50817d8d9b307ba7942aee95804 *man/barcodeData-set.Rd
5609ac0cd3f5ebfd864f34b08eb7e5a6 *man/barcodeData.Rd
c9502b5e1bf27c6fd26dc56919ce2ce4 *man/checkConfigFile.Rd
6f320076d679c374ee8b57bc0f72d0a9 *man/checkFileWriteAccess.Rd
4607f2749552b4f765d06bc11b1d7015 *man/checkPrimers.Rd
4899e559d8e5c04f8dc9eb77057ccab3 *man/checkTarget.Rd
977f5b3d0e9ec7111b302baeec25afe8 *man/cigarsToEvents.Rd
ce59a5c7afe57aedcceb708eb1522dc3 *man/comb_along.Rd
ea362c6eaec39de33e1b9d2edcacf632 *man/cumsumw.Rd
772ad06bf18be6eee0809df3e3044c85 *man/decode.Rd
6330eaddc1d4014780ad9addb96997fd *man/defGR.Rd
377032e6df03207d0fa82a463f7508d3 *man/experimentData-set.Rd
67c11080eccb6e8ec8ab92b8b18d94a5 *man/experimentData.Rd
6f0766d7a68bedf2731f3525c0248757 *man/extractEvents.Rd
4f44d2219cd60edc8cc2bb85eb60336d *man/findEOP.Rd
195526fafa881bf32b47b0f8b8d73dd0 *man/findLQR.Rd
e90bf1bd184527b6ca1d3a12fe8bcc0d *man/findPD.Rd
606f28be115b3b65757102db597e0048 *man/flipRanges.Rd
0b360116f5c7a8cc02be8a3472a07e41 *man/fwdReads-set.Rd
b8d400d59786c6c8459b75040fcd89d9 *man/fwdReads.Rd
cb3fc704d9b0b00c3d1f91b8e08c6917 *man/fwdReadsType-set.Rd
743796f12c2e4d39e459f59b5ce63b25 *man/fwdReadsType.Rd
49bb6869936f72f7f78db7e9f35fcc4c *man/geom_bezier.Rd
c4dcbd5aae7a5fd64ab1145e632e3af7 *man/getEventInfo.Rd
b4bc86975f1ef884f5946fcea7d0f587 *man/getEvents.Rd
5b0b91c6a815be888a7748878f988c89 *man/get_left_primer.Rd
30b4925cfb208c69e26c78313abd5391 *man/get_right_primer.Rd
38185256a942579ca5d3490305cb2980 *man/get_seq.Rd
fbc72a463910c3b56a059955cbd27210 *man/goodAvgQuality.Rd
610edccd5233d267a38a6f1d1910c0a9 *man/goodBaseQuality.Rd
e418f1e97da632abc490111144c65e27 *man/is_hdr_strict.Rd
e8fb92cece26956ec7a2b3a26cddb6ce *man/locate_pr_start.Rd
306099823b4450160354b25a47fb8fcc *man/lookupAlignment.Rd
5012c5d2ecceeb7821bcaef8502cad3b *man/makeAlignment.Rd
f4a662055c538314bcaebddcabdbc43d *man/metaplot_deletions.Rd
fda72625e1ff282d33aa14eb49c77e31 *man/metaplot_insertions.Rd
e870c65e9664c033ab2f23ad26674d3f *man/metaplot_mismatches.Rd
93b090d3f87d08ee063a9a3354ce04ae *man/pairToEvents.Rd
6f0c9b1f082cad5a4e43371adbf0448e *man/plot_amplicon.Rd
3880abf770d0cfd9b78041593f8a0470 *man/plot_cuts.Rd
dd905d804c5bf18c8ed8932df9894e3a *man/plot_deletions.Rd
cf42b00e205a2b19bb77d097c5688719 *man/plot_height.Rd
89630cf03e13a66bc372b24a3529e866 *man/plot_heterogeneity.Rd
2bb2856a58eb0e9f8ad87d82752fea1a *man/plot_insertions.Rd
9028a6eccc56403945004b3ad6e0a2d6 *man/plot_mismatches.Rd
e9e4d9e330959440d3aac472d6cc7544 *man/plot_variants.Rd
138db820c70b21a51bcf7913bea63f6d *man/readCounts-set.Rd
260be1fc103b0339b709b4f5b957d111 *man/readCounts.Rd
f9f04d4bf08e48d4168cf9518c78f369 *man/revComp.Rd
e3a11a6cb9503ed9fb5b234093921b5a *man/rveReads-set.Rd
b82c763f88b9a5afcb441f59d212a984 *man/rveReads.Rd
dbeedfff5bec58fdeb0ee747d30cfeba *man/rveReadsType-set.Rd
47b3498bac9d53efb948bdf42c4ce8f8 *man/rveReadsType.Rd
3f60a744ed20ae0b8e62a6bf0871e2d0 *man/unassignedCount.Rd
14a98f96e482c98dffabfac177f69c04 *man/unassignedData-set.Rd
3cc713e6dba023359f4deaca907427c0 *man/unassignedData.Rd
ca1eb9eebe4d35c2636e930481cd6f5b *man/upperGroups.Rd
0196bdd14d579cfc8330175dd1f8d27a *man/waffle.Rd
e5f90213b742fb950bd77fcfbad805ff *man/writeAlignments.Rd
3f62c2f38dbd96f3cbc964a58345631b *src/RcppExports.cpp
5d1dc745394f636ee366fcd3eb267879 *src/bezier.cpp
20422cf7212cf396d54b0fadf1f7090e *tests/testthat.R
39602a6fc9299aae95f8363d49376fc2 *tests/testthat/test_alignment_helpers.R
7bf47ceee3708f11da44feaf982871e9 *tests/testthat/test_amplican.R
45863f2ae2b03ce1ae760299b4a83a55 *tests/testthat/test_filters_helpers.R
35a1b4fbc10c0d35264ca85dd70ed422 *tests/testthat/test_general_helpers.R
846da3f8339eab0072dec624fa1585f5 *tests/testthat/test_plot_helpers.R
18d9c9dc17e8bb44e876d564c73736ee *tests/testthat/test_summary_helpers.R
22c1153df9da5aa066349a91dc711272 *vignettes/amplicanFAQ.Rmd
9c058f3451b48b21c910902bd51abcdd *vignettes/amplicanOverview.Rmd
3fd3b92ac65ce84ec1cdcd21533a77c8 *vignettes/example_amplicon_report.Rmd
676b4ae6b2cb7d23445352a050a17417 *vignettes/example_barcode_report.Rmd
aba57432a7223a5da60656dbb1ea627a *vignettes/example_group_report.Rmd
0c21776dd3b473f272ffe532821a7f3b *vignettes/example_guide_report.Rmd
0c8cd614c82f4c62c1f259fb3363120f *vignettes/example_id_report.Rmd
657b7352c13fe03e8c933edeef3fcb3b *vignettes/example_index.Rmd
d8da2d04352c679f9d09dc1f762710fe *vignettes/figures/amplican_conceptual_map.png
12cbaa674f8ca638862d82a6b1b641dd *vignettes/figures/amplican_consensus_rules.png
302c86aafc5d24590137191d9411498c *vignettes/figures/indel_rate_vs_indel_size.png
