2026b3cf134fb8ea31b225d8b1932c43 *DESCRIPTION
101b9541ba63e29bf2ed74be48dab987 *LICENSE
ab32331660795b775ae0ad383404b789 *NAMESPACE
964dd1d0f6085dd6b222841fe73f335f *NEWS
7b6b321e75348e9747934ae792374b73 *R/DOTSeq.R
064d4f912e9b0dab82c07186ff3ba855 *R/RcppExports.R
b5ab6a073e4c61f8727afccbb6826a28 *R/annotation.R
cbe99ff867df025bc3c23bf212285dad *R/classes.R
e2b6b664c00947e4322e64af041464c3 *R/data.R
31bc2dda878c15bedafc9a4e3d30f051 *R/fit.R
a51712d3d3fe2fc2a157f5648067e27b *R/formula.R
ff8e1e30f7bf8c27850cce4b71fded24 *R/main.R
7f81b448f86bda3308a4997e70323e60 *R/metrics.R
9e31ca4c5cf8113589f290f81dd202ae *R/plot.R
9325c89dc1a1c1c2f203bb87d00ad1f5 *R/posthoc.R
5dafcd846763743f8366e4db59d07e32 *R/runtime.R
edba401900983e37f5ce2abb23f49077 *R/simulation.R
37caa7dda949e1a85ec7c533b2d98e73 *README.md
533839446f70bde34a1050627ce80586 *build/partial.rdb
1cf03d1bf3ec6e308cd7bc7e52393df5 *build/vignette.rds
8e56822d29f1fdfe7ebcc94fa5fed6e9 *inst/CITATION
a05b63db28092979dd566bb05b9d7a7d *inst/doc/DOTSeq.R
b93a28a31e8f56504efccb73407a4d0b *inst/doc/DOTSeq.Rmd
39f773da02c06e55822af24c8bdab6e9 *inst/doc/DOTSeq.html
d78808ae0cdb33c35060cf9a66c823ab *inst/extdata/featureCounts.cell_cycle_subset.txt.gz
77fbcf5fc015ad113aa65b01b8667638 *inst/extdata/gencode.v47.orf_flattened_subset.bed.gz
904787f78f9b350e1a6e5ec0a4677020 *inst/extdata/gencode.v47.orf_flattened_subset.gtf.gz
eaf46ce7a23b22e88c2938fbb78a5580 *inst/extdata/metadata.txt.gz
3dcbb520cd5c79ec9c29d8a8d11e162d *inst/scripts/generate_extdata.sh
f7419c6252008c0331fac6e9093fb460 *inst/scripts/orf_to_gtf.py
16c4aa5b044f497c7bc16fcd36429ce5 *man/DOTSeq.Rd
0b28f8635f29ad60bd59f578fcba5b1e *man/DOTSeqDataSets-class.Rd
ada81e70de22f501671a4956b33e74c7 *man/DOTSeqDataSets.Rd
fba5b5c22824196d3a7f9538700a1368 *man/DOUData-class.Rd
3e2795ccdffbb1e0f5faabfce03de608 *man/DOUData-validity.Rd
01d1c1f6bbd59e2243469d1f6559c84f *man/DTEData-class.Rd
8d8827c8fd59bfca939369056be779a7 *man/PostHoc-accessors.Rd
2ea6991b385d6365a249982dcc708fee *man/PostHoc-class.Rd
bf2d4f36a155f6597bc469cb7303c8f5 *man/PostHoc.Rd
1c61e3373e8fbbb5c6ee532858721739 *man/annotate_orf_type.Rd
d20565ed2ee7388c2503dca304d812f8 *man/assign_strategy_levels.Rd
2b95d5902f964dbfff1fb1ea6ac217f6 *man/bm_use_ensembl.Rd
0e82835518b023adf518637fa0f846b1 *man/calculateTE.Rd
c213be4a882184c616ed5ad34a64d5b0 *man/calculateUsage.Rd
e1e4b1fc30c6da4870fedd23d5ab633f *man/calculate_mean_dispersion.Rd
64157ceacaa69d5341b173e1d7a2bed5 *man/cistronic_data.Rd
664b4c7a880ead11bf9b5f38b518cf76 *man/contrast_vectors.Rd
7c668aa86c5d059a6f12232a4381df78 *man/countReads.Rd
c23480d1c947141d6b3a9be8b5b3b571 *man/countReadsSingleCell.Rd
faa0b68889e0305616ed5dedab8469c7 *man/create_datasets.Rd
d2c47ab818587928185b69ec2b073797 *man/create_read_numbers.Rd
e13c4967dbcb3b6a0514b2be8cd8bbb5 *man/extract_results.Rd
e0f61ba529547c89723486fa21b7a815 *man/filter_gtf.Rd
1ac852213f6783a5e9cf36ada107970b *man/findORFsFasta.Rd
98a0983fd50c64577361538c04f4fd59 *man/fitDOU.Rd
206b9b4ece0e1318b5583cb86d6e3bff *man/fit_beta_binomial.Rd
c1cf3c121722965ffe16562141fc9faf *man/fit_glmm.Rd
86b69b8122ada7d3c68a8dbef4df806c *man/fmla-method.Rd
7530c108d33d19aecb43ca13a24030b4 *man/fragmentize_pairs.Rd
c884656069b66de62c3c945044a129f7 *man/gSort.Rd
006a16ed592ea2764ab918314f06ddb5 *man/generate_coefficients.Rd
0555b621e906584167e0606363254b8d *man/getContrasts-method.Rd
c3963359272c85d82f5945b38d911b34 *man/getDOU-method.Rd
fd6544b139dd9f5e5069965e98d59f3f *man/getDTE-method.Rd
a1a73ff986e30396e65a46c1f1aa125c *man/getExonicReads.Rd
65fc85432161653a79ed00ce0b3b49a9 *man/getORFs.Rd
61da663ff24f0b221fc1157c8c90f731 *man/get_lfsr_annotation.Rd
2f2287c0fdbfc26fbca2d063ec9fb7dd *man/get_params.Rd
3970d4e4be78fb7a1cf56ffd863e8924 *man/get_significant_genes.Rd
b28e3d232df5f01ad5299ae68b680617 *man/group_bam_files.Rd
7173a48f591fb315327fd379a52f543a *man/is_paired_end.Rd
498984081d026732984a0dc568d99dec *man/lastExonEndPerGroup.Rd
a994c9737ccb58f95053d4d5ced5cddf *man/lastExonPerGroup.Rd
5b7ad3d972c0e1e3fa480e8fdab7287b *man/lastExonStartPerGroup.Rd
da1a4781240b939e7e56987077798658 *man/longestORFs.Rd
dfd55a009f5aad146f9b8f6176f97f60 *man/mapIDs.Rd
eeccdc2997ec38e1be663345d297e23f *man/match_runs.Rd
bf06e4d7b6f77bafec16da3640d23849 *man/numExonsPerGroup.Rd
fa6e543255d3e905ae167e2a1131512f *man/pad_cols.Rd
2f40abc40467c275c7662f00ee300624 *man/parse_condition_table.Rd
0c23ab113e2643c76167e6fd1aedaabb *man/plotDOT.Rd
8248a279a6d00ed64f01a30543e02069 *man/plot_composite.Rd
bff753c19368393b213bf84671984aa8 *man/plot_heatmap.Rd
ef68e464135c7a75bcbd28ce672d8b93 *man/plot_orf_usage.Rd
5e515396992fb1f1ef27d04a9f8102e7 *man/plot_pca.Rd
d4537d65dad35efb455e33330fc333fb *man/plot_venn.Rd
980a4c82de10ad7b7cad92154d22015a *man/plot_volcano.Rd
d96b03262b210e60da70f114ba5f3a8c *man/reduce_formula.Rd
e66b24dcef5005bd4aa9dec2a1c3eeac *man/remove_random_effects.Rd
3a4b41146ee4ff3774d75d3059ad7107 *man/reset_graphics.Rd
5940260f3fa70d12e092610fce7fea32 *man/reverseMinusStrandPerGroup.Rd
5bf27e36ba03d80a6986a828f72c4be4 *man/run_diagnostic.Rd
3187e1e17494760b77d3acc1e8d9b6c7 *man/runtime.Rd
77efc5026cedabd17b06d2e4358a8522 *man/seqnamesPerGroup.Rd
e46d09c342ffbefb0396838c01eb7bec *man/simDOT.Rd
cb270f8b1887533c06ec7d8db2907477 *man/sortPerGroup.Rd
f3454344d7091d012d0bf8b9f9ed1918 *man/specs-method.Rd
e1cdb11c6152832f1bff84b52c55da8f *man/stopSites.Rd
1ebac330b16dfc9af1e8a353a0a0f639 *man/strandBool.Rd
ae38453202d6f38aa304adc7b30ede53 *man/strandPerGroup.Rd
d15cb86528abc59e53773326ed5cfddc *man/tally_chunk_vec.Rd
cd274e1a60d5868f4556706b3390a5b1 *man/testDOU.Rd
392b814a64c35fa8bbf045adc90021be *man/widthPerGroup.Rd
504005fd6b78d67d36fbd57078d68fcb *src/RcppExports.cpp
24d2953dde2d1f4ad5bf64b9269cc3e2 *src/findORFsFasta.cpp
8b11feef7d13e8cbeb4c9215b527e5b2 *src/findORFsHelpers.cpp
b73e2a039307c88b9ea4408541885e44 *src/findORFsHelpers.h
8bf46333dd9bf3ca0a12c838615ed76a *tests/testthat.R
18ea1bab8b6e3b6d810a1c3166e55651 *tests/testthat/test_DOTSeq.R
ae0ba3d20af892b1f975f3800b320457 *tests/testthat/test_DOTSeqDataSets.R
e01d7415cb1ed1e8a077dd9d9875b55e *tests/testthat/test_calculateTE.R
0c678e2edcb76becee1a2a436fcdc8fc *tests/testthat/test_calculateUsage.R
557c7c8274501e8571d509f9beafec96 *tests/testthat/test_countReadsSingleCell.R
b9836c1ef86d6f797818526c35601049 *tests/testthat/test_filter_gtf.R
ff1ee459e94b09d8053e18adeac22439 *tests/testthat/test_findORFsFasta.R
f2332534b811431958db3a2767e8fcd5 *tests/testthat/test_fitDOU.R
657aef7c42fd659a7f0ffa7b6bdf5bc3 *tests/testthat/test_getORFs.R
1d6078d6f89b66169e2b19760a4c4e26 *tests/testthat/test_get_significant_genes.R
4a281b8f435187f9c318b1b0d9032b82 *tests/testthat/test_grhelpers.R
ee8115680d339caac1eb94df36658c81 *tests/testthat/test_mapIDs.R
2c3af09f1d7ec2ad15c8ba661a0647bf *tests/testthat/test_plotDOT.R
75ddd5ff87f6f040ab8c4893cee2d9c4 *tests/testthat/test_reduce_formula.R
6a4c33d97211df7a70181a919f24b761 *tests/testthat/test_runtime.R
1b40cc18b9f3d50a970c9e5f8bc4e1ac *tests/testthat/test_simDOT.R
4dd544995dc457e1eec4e72a3a873b16 *tests/testthat/test_testDOU.R
b93a28a31e8f56504efccb73407a4d0b *vignettes/DOTSeq.Rmd
64bc7cd53dce875dba041aaae5d362fa *vignettes/DOTSeq.bib
c352e2b83596d058a0d71ca17ea3b34a *vignettes/nature.csl
