9d3d38b1ae9bfde5ced918dc7d94ed96 *DESCRIPTION
80814dee6b81d6dc8e8926a52d424fe6 *NAMESPACE
af4985a098311f8c5d2b444c68cbe4c1 *NEWS.md
b31b156f3a3b8858838a2d052e8682eb *R/DuplexDiscovereR-package.R
a723cd9ef80a6907ef5a974f05f71172 *R/DuplexDiscovererResults.R
b01be975fc7f950796f5b2dadab7f417 *R/DuplexTrack.R
68df247897bf483e66acbc5074135540 *R/clusterDuplexGroups.R
23b30174b6f991f87fe49a3516dbacc2 *R/collapseDuplexGroups.R
f9b3022bc47369eb1415c6de4c89f83a *R/datasets.R
56201c78b823a1489e9ec395ed61b646 *R/getRNAHybrids.R
452d4568f1b17bebddff9fa623a24cb0 *R/runDuplexDiscoverer.R
26be7a2bd5c4d687d3b9db26b1691ae3 *R/utils_annotation.R
da9e63d65b21aaa9bb676a048e39ccbc *R/utils_classification.R
d0349dfeb2cf1e58064bb2a13b0e6e74 *R/utils_clustering.R
ad45436f4f2ae1d4da13a3b0cabdfb30 *R/utils_comparisons.R
629c99312114288e5bde1bc555f7adec *R/utils_general.R
7a0e976b90cfcee739e98a30c0755967 *R/utils_preproc.R
5a6b51a910c420c466d2ed5691a9c9c3 *R/writeGiToSAMfile.R
40b0755f73566646a32e54d00035cb9d *README.md
e2f77945f1d6587dc7bfdf722eb92126 *build/vignette.rds
ea30e29f552b6a35508dbe2c03bd0664 *data/RNADuplexesSampleData.rda
6c6e83f453f2a233d79083b5f2ff45a5 *data/RNADuplexesSmallGI.rda
fdb5a59ab74e663c58ddf439899c6c90 *inst/CITATION
191d5102c72fcfc7c4cb464f54bcd165 *inst/doc/DuplexDiscovereR.R
a6a3d189f1d53a5a349c26b31b0547c0 *inst/doc/DuplexDiscovereR.Rmd
187e843b3662f1d667d621928a3b293c *inst/doc/DuplexDiscovereR.html
98b1d4101210fd3f22bc3b6dbc4e7e1b *inst/extdata/example_artificial.fasta
4ebf3eb05a63880323f136a4d86f1068 *inst/extdata/test_SPLASH_Chimeric.out.junction
b4071dd1ef611e17bb4fa2b89ed55dac *inst/extdata/test_SPLASH_DuplexesRaw.bedpe
cf8db45f16c3e7007f22415bae2865f3 *inst/extdata/test_chr22Anno.gtf
a96395788fe3322b5e42d367321436ee *inst/extdata/test_chr22SpliceJunctions.bed
6c37e0a2ced3e833a6b1ee8e0408983e *inst/extdata/test_geneCounts.tab
5f31be3604e01a20b29b573d468eca11 *inst/references.bib
0beb0743913f816e22bc2e396182ed30 *inst/scripts/DD_data_generation.R
495aa1feea5b6ae479ce7d98c4d65ebf *man/DuplexDiscovereR.Rd
61e88c702babaec81e269609b0d48fc3 *man/DuplexDiscovererResults.Rd
263844ab591ab25a937e3969c7428a05 *man/DuplexTrack.Rd
a6a35e5949a380af8d65fb0dee6bf5d6 *man/RNADuplexSampleClustReads.Rd
34e996859c42a66f2d7f158921ba602a *man/RNADuplexSampleDGs.Rd
1ab8375d7fae2f80793ca633bca6ad15 *man/RNADuplexSampleGI.Rd
e4f1a1b9347bafcdff7568d4ae29d085 *man/RNADuplexesGeneCounts.Rd
e9211f7d134e343b982df4b32a703be2 *man/RNADuplexesRawBed.Rd
bfd6f1b9d08c3bae292bf43d785a5eff *man/RNADuplexesRawChimSTAR.Rd
a847d81a80246e8cabb06ed22e2a3791 *man/SampleGeneAnnoGR.Rd
11a250167b802bbd2b1d4ae3df4d0ee0 *man/SampleSmallGI.Rd
54a41c4672bed656772664b5acb72b18 *man/SampleSpliceJncGR.Rd
86eb17966595f5057089796c0b51f4cb *man/annotateGI.Rd
1f5cf0b26f2bf740be6c913c2a2ac86e *man/availableDisplayPars.Rd
68ba71d3511627bf8631cd1a78743cbe *man/calculateLigationPvalues.Rd
574de50ab4785b68210d48d2c6dbef7f *man/classifyTwoArmChimeras.Rd
65d867f70fa21064d143b59c9bcfaad0 *man/clusterDuplexGroups.Rd
79da2d40f0332697038b6aca57aff066 *man/col_check_rename.Rd
076bfb9d97328cca45e87d9edb122e86 *man/collapseIdenticalReads.Rd
d4589c76242980d5807402a83fd4e95d *man/collapseSimilarChimeras.Rd
f23ccd1709b0994acd72d7ff3609aea9 *man/collapse_duplex_groups.Rd
ef083b10be59cd0ceb91dcc5490d3bfe *man/compareMultipleInteractions.Rd
7f8a53bf264077aa3147fe76b0ce1d04 *man/computeGISelfOverlaps.Rd
c288adf8b7f588382409c5871efa1629 *man/convert_gi_to_ranges.Rd
3b459749332754ebe8c08a3010bb1081 *man/dd_get_chimeric_reads.Rd
0ccc5c2e3e06369664840c507e366f54 *man/dd_get_chimeric_reads_stats.Rd
28f4fc786a6bd77a804ac6f4898b6eee *man/dd_get_duplex_groups.Rd
43afbec6c004f81ba659143ebc7bccc7 *man/dd_get_reads_classes.Rd
334f1888cee63b4382bc8094adc6fe2a *man/dd_get_run_stats.Rd
dbd8830b49454ede4b32e56556cd781d *man/dot-DGIdToDuplexId.Rd
62adc542d420771ce9b2b4b051fd5261 *man/dot-addDGidsForTmpDGs.Rd
cda9b2037e8e82b19013ce5b8fa04d95 *man/dot-addGeneCounts.Rd
18b661b226953f176e0400c1a28c745f *man/dot-annotateCisTrans.Rd
7f25c4f702f0b92c13f90105549d04a2 *man/dot-compute_clusters_comp.Rd
dbe6b0fbd0400f4739787983d31d80e9 *man/dot-getStartEndOvl.Rd
8c5c1b97f44fcb61875043d61ac6b158 *man/dot-gv_plotboxes.Rd
4603e79f3c373c760da30f8999ae5e27 *man/dot-gv_updatepars.Rd
786dab71252cebc61f4c354ab750585a *man/drawGD-DuplexTrack-method.Rd
75511adff445933908121306f0bea0c6 *man/getChimericJunctionTypes.Rd
210d04be9d0a26c00f369b95be6edafc *man/getRNAHybrids.Rd
25a6f29ac11f40469c9ffba81dfa4b7e *man/getSpliceJunctionChimeras.Rd
c5c0d11d4bcb4a140dff73de59fa6d10 *man/get_arm_a.Rd
2fc297b5be8e0d1ff975dd5048554be9 *man/get_arm_b.Rd
a8b75c65dddee4933d03abd75d63c015 *man/get_char_count_cigar.Rd
8e2e8700a3f247e07656b5e61ea481df *man/get_chimeric_junctions_onestrand.Rd
eaaebb934026bf5fc5cc6f18cbf6d8b0 *man/get_colnames_and_types_for_input.Rd
4a2775c3985a31b2e8cca192a7bdb476 *man/makeDfFromGi.Rd
45385096e04b84d032122cb979cca496 *man/makeGiFromDf.Rd
28b59282b2d4f72f85f0f187ebe93732 *man/preproc_chim_junction_out_pe.Rd
218fd75188a12ccc3b8fc7c6662efcd2 *man/preproc_chim_junction_out_se.Rd
4077360855c911e0c114d1283cfcc986 *man/preproc_generic.Rd
ad0617f60da9288c1e5fb1fc01420d59 *man/preproc_generic_gi.Rd
527f8740443db31b8cc3ce8628f0bf62 *man/refresh_gi.Rd
30f72aa3ce7748e155a16716222a6b78 *man/runDuplexDiscoPreproc.Rd
6eb9dcbf76ec9ff5d41b83d8c1be47e8 *man/runDuplexDiscoverer.Rd
47656774efcec0542dd7480b4ba6e413 *man/show-DuplexDiscovererResults-method.Rd
6fe2ea053f28eb876a0079c56848d061 *man/show-DuplexTrack-method.Rd
c69ae0cdd833e37eafcfd954c652d42c *man/subset_gi.Rd
d1ad710c25090af0409e2e83e6dc218b *man/trimAroundJunction.Rd
71c409acda83613005d9cabf29ba146d *man/writeGiToSAMfile.Rd
5221e6523f2f849fe968c4bcd629e3dc *tests/testthat.R
4598ef15d24f641c076a4f0884e9a88f *tests/testthat/test-data_load_and_clustering.R
aa58ccf1e75c93e176e22f94aa64284f *tests/testthat/test-test_run.R
d8791a1d375b6559bb6fbd5d91a95dc7 *tests/testthat/test_comparisons.R
41539921f6e92baf63be9460c2d8f1af *tests/testthat/test_sam_output.R
5a06965123b48f72bb8872c6ae305095 *tests/testthat/test_viztrack.R
a6a3d189f1d53a5a349c26b31b0547c0 *vignettes/DuplexDiscovereR.Rmd
