8c044070771dc2a0317fcdf88221759d *DESCRIPTION
efa446d7dbe843a67aa0e3cfb0108cef *NAMESPACE
fc2a7b00ae32c8097370750129c83f25 *NEWS.md
f50385f1b2bfca753d58e61b4f4ee68f *R/AllClasses.R
d674f6a5c2f5f075785c02518ef272a3 *R/analyse_go_terms.R
06aa1cd2d726400cdf23af665fffdb31 *R/browse_igv_regions.R
a0fca4cc216d9281708cb3ce7b306f9a *R/damidBind-package.R
9acbda59ffb5ab6dcb3dd383286f800a *R/diagnostic_plots.R
277471153a107fadacbb66897127e93b *R/fdr_calculations.R
08bf8227423c5d4d00dca2f3048b7403 *R/get_ensdb_genes.R
67439ec82901c883e52f18fae31859c2 *R/globals.R
47a219da2c2bcd08691c70ac0c2003ec *R/granges_functions.R
ed4e95ed320b278eb0cf216c6e08962a *R/limma_functions.R
5527ee30b0de79a81e64155ca9f86106 *R/load_data.R
7017765eab2080ddcc87e893c0d1e3df *R/methods-DamIDResults.R
9d488d6861a1b4cfe1607d32c5910781 *R/noiseq_functions.R
2c92b2c77fe6d7eac31e1970711483e1 *R/plot_venn.R
0064fcae1d32d41ba2099f3d729c621d *R/plot_volcano.R
875996b1deebcc646cd94772e8b9830d *R/prep_data_for_differential_analysis.R
23ba755dd50950ed9cd923fdbd013e92 *R/quantile_normalisation.R
fa4000dc12d445ceca816379c4a1bdb7 *README.md
41863622d6bcd1992717b2dd52fc576b *build/vignette.rds
4abcd28c852294ae1fbea286c08bba5b *inst/doc/damidBind_vignette.R
a271b42e334cd1b1a701cc4ef9fb23c3 *inst/doc/damidBind_vignette.Rmd
9f775507bfba6f10519e34766e950df8 *inst/doc/damidBind_vignette.html
d7eadb82ee8e3e73b2b68ae6bac9b2d4 *inst/extdata/Bsh_Dam_L4_r1-ext300-vs-Dam.kde-norm.gatc-FDR0.01.peaks.2L.bed.gz
8533bc59a3e6fd5bd377aff49cc33384 *inst/extdata/Bsh_Dam_L4_r1-ext300-vs-Dam.kde-norm.gatc.2L.bedgraph.gz
9dcbf94efcaf3adb86e57d2712d1d6b7 *inst/extdata/Bsh_Dam_L4_r2-ext300-vs-Dam.kde-norm.gatc-FDR0.01.peaks.2L.bed.gz
4c2451d3333bcc2bd53564c76dfe5673 *inst/extdata/Bsh_Dam_L4_r2-ext300-vs-Dam.kde-norm.gatc.2L.bedgraph.gz
a084fbf34873c90d76fc639238d62a66 *inst/extdata/Bsh_Dam_L5_r1-ext300-vs-Dam.kde-norm.gatc-FDR0.01.peaks.2L.bed.gz
ba2cc1d34a3da94066b46f0146742874 *inst/extdata/Bsh_Dam_L5_r1-ext300-vs-Dam.kde-norm.gatc.2L.bedgraph.gz
30da897cb925146f573f5446a0b0afa4 *inst/extdata/Bsh_Dam_L5_r2-ext300-vs-Dam.kde-norm.gatc-FDR0.01.peaks.2L.bed.gz
f2a7badf678a6b0868c8a3159af47ebe *inst/extdata/Bsh_Dam_L5_r2-ext300-vs-Dam.kde-norm.gatc.2L.bedgraph.gz
fe1ff9c8301678566206764a20c5d47e *inst/scripts/data_provenance.md
dcb7235c7d890a32557b1cbb3d47d314 *man/DamIDResults-class.Rd
35151d23b6de85dd6bb0b1299b572a16 *man/analyse_go_enrichment.Rd
e3922830e149e36d3cda884910daaf80 *man/analysisTable.Rd
722049269112754cb49fa42829a107d2 *man/browse_igv_regions.Rd
a8688fe9821b85a8a3a849f97facd049 *man/calculate_and_add_occupancy_pvals.Rd
c0f333f3f53f39ebca4fee17e6b5e8e6 *man/calculate_occupancy.Rd
d0cc77fe5114c6f471a0b66ed2283d75 *man/conditionNames.Rd
b1fdeb95a1011448477467abad73bf7b *man/damidBind-package.Rd
abf78c033dc041caeaa38a9acea576b3 *man/differential_accessibility.Rd
ba5449bec8184feb4886f207e0dca2bc *man/differential_binding.Rd
a4dec5217c57c1d12e32dfb1b4feadce *man/enrichedCond1.Rd
97671d51c54d139d1b073ec5ac5ccf2b *man/enrichedCond2.Rd
3d4c7dcc9f5ffb34ca92abe7053b64fe *man/expressed.Rd
485d6c698f72a3eea5c878ad5867f4bd *man/extract_unique_sample_ids.Rd
bd312ca2b445327d28269b37cbbc1fec *man/filter_genes_by_fdr.Rd
a229492d95ab27a80563c29f2a0cd542 *man/get_ensdb_genes.Rd
766993d13307139a38b4fc4cf9bca5fc *man/inputData.Rd
8cee1dc7612cdc95d600e9e573393769 *man/load_data_genes.Rd
484e623e37d3086607719e567fc3fd87 *man/load_data_peaks.Rd
f5fae29e57feea72809a2111ba71b5a4 *man/plot_input_diagnostics.Rd
118bce4acfc99236d5c75363bf0633d4 *man/plot_limma_diagnostics.Rd
bcdfb4f2f16e614db176d4d1134e8406 *man/plot_venn.Rd
c88849e9f59b2a3a332c6cf1cf7d035f *man/plot_volcano.Rd
080d751daba963f105590d66bffa1410 *man/quantile_normalisation.Rd
1c8827281c13a2b43d78582c307b5b68 *man/reduce_regions.Rd
b3b472829dabba81bda0d21c55dd1bbf *man/sample_labels_by_isolation.Rd
3411cb70f5580f7acf579518b738228e *tests/testthat.R
45c9b669f6e0b173159008f52deec7ad *tests/testthat/_test_helper.R
275560d2db461b9f81cdfcd0a47a4d76 *tests/testthat/test-DamIDResults-methods.R
e5fe461b5ff658997be7395b5cb21945 *tests/testthat/test-analyse_go_terms.R
8bbd77ce905f84578222b2ed048b411b *tests/testthat/test-fdr_calculations.R
5d827e6ba420c1fe6766e668eb9d8f4d *tests/testthat/test-get_ensdb_genes.R
0ae8198e7a978deb6947ee92be90d87a *tests/testthat/test-granges_functions.R
23f20f342faee328c94d7b21c10ad20f *tests/testthat/test-limma_functions.R
22bacc8a854760e187b1ca5901c869d7 *tests/testthat/test-load_data_granges.R
5f89bec7ce79db171d45886327b63a32 *tests/testthat/test-load_data_peaks_genes.R
c274800e3569656517eee265e9cf7bc6 *tests/testthat/test-noiseq_functions.R
a90bfa5de10637cb320f0543fa8288bd *tests/testthat/test-plot_venn.R
c0f05cedfcca9edab9a71ddb3939c0e4 *tests/testthat/test-plot_volcano.R
64b115f853c6d2cc4ca73b8f94052147 *tests/testthat/test-prep_data.R
b399f4138f6d5d6091fe942b929288a5 *tests/testthat/test-quantile_normalisation.R
7da928da8bd9348be5373d8f1ce60155 *tests/testthat/test-utility_functions.R
a271b42e334cd1b1a701cc4ef9fb23c3 *vignettes/damidBind_vignette.Rmd
7a640c7d9c238f7b9d10065e08626eac *vignettes/damidbind.bib
41f0a40342925d87871ff7d5c12c6c19 *vignettes/embo.csl
1aba153823950b3c04ff71e102966814 *vignettes/figures/damidBind_L4.png
d79ef02fbe9d2d2a22d7a99557da62e4 *vignettes/figures/damidBind_L5.png
3e2f2f48bcccab82f028197e18079bfb *vignettes/figures/damidBind_igv_example_2025-11-29_18-20.gif
44fbd0f41ea3830be6af6b721cb24398 *vignettes/figures/damidBind_igv_example_2025-11-29_18-20.png
9a2438d314034daa083db729069bd951 *vignettes/figures/damidBind_main.png
