a78548e6e9106bb42046b217ad897ec0 *DESCRIPTION
c3527c2b6969f7645599911bc0d86e70 *NAMESPACE
6747a781c4513731eafbaabeb7bc9378 *NEWS
856659041a957ccf6ff50ee035ad0828 *R/CleanBAMtoBG.R
f9c0088e0a750db85c2f83d93bef5804 *R/CleanBEDtoBG.R
8201e8aca5887d45afb68610db518c97 *R/ExtractTranscriptomeSequence.R
1fea55069cb37c6ccc7c06838d820e4c *R/GenomeMappingToChainFile.R
bd1871a31374a8ccf7e936045418bb34 *R/assessGrouping.R
b542eae825f15e5bd5e5d28af176428b *R/bindingContextDistance.R
bc725f48852bca1dd165f5c29fedb3d3 *R/bindingContextDistanceCapR.R
441b4750b399f3afff9a9e81b12399e9 *R/getChainChrSize.R
3d04bf862b3a9674893627c33005d13d *R/get_outfiles.R
a735cedcc96c1548341bdd1a1d0eb881 *R/liftOverToExomicBG.R
d57b28558edc5f0c807952304c0bd719 *R/processCapRout.R
1ba218b4f21e91f7b41e752b088a2549 *R/runCapR.R
5019525ccdf229c1141940f2fb25c99f *R/runStereogene.R
da7cc969b6d2b0f876b9d58541bec468 *R/runStereogeneOnCapR.R
12cd39b0f79e4317d8fe1d7fe272c6ef *R/symmetryCapR.R
607893644acca10340faf5058dc6ee7d *R/symmetryContext.R
b8af7e5c017943b7c42301bc8b8cd407 *R/utilities.R
a98f62e212587189e8303bc92267ed74 *R/visualizeCapRStereogene.R
12f07f12f44fdd05703f4fe842f1adac *R/visualizeStereogene.R
b6385b4345c34a6dd0dca303f5abf8e2 *R/write_config.R
d31b4eee7bc251bb2c45ed6921212b4f *R/write_fasta.R
e6705a7cdafb769375c742a08c0e1f7d *README.md
5c050e0f094f1fc4b158547244fe9269 *build/vignette.rds
8398526f965b85b38952034e3d9f4648 *inst/doc/nearBynding.R
80c1debda56a3692ad5c95eebf6a39c9 *inst/doc/nearBynding.Rmd
18c469839ed6bd200f4326963ea8cc31 *inst/doc/nearBynding.pdf
ae6d7e4e4567a736e0ad90bf0511069f *inst/extdata/Homo_sapiens.GRCh38.chr4&5.gtf
a1d705288a73dcc27ec57d42817afa82 *inst/extdata/bulge_liftOver_chr4and5.dist
7da5930fb5148f0a236ee301e41c951a *inst/extdata/chr4and5.bam
ac452d2dcc2e0cbdb3b6b1dc944b03a2 *inst/extdata/chr4and5_3UTR.fa
133d71d3bb199112646fbddcfa265a23 *inst/extdata/chr4and5_3UTR.out
6c14d3f68c7d0733bd6cbb64bb80da1f *inst/extdata/chr4and5_sorted.bedGraph
cc2198191dfff58a31a6791f59374199 *inst/extdata/exterior_liftOver_chr4and5.dist
c346782659cbe9dc0b8c609cd0694b3a *inst/extdata/hairpin_liftOver_chr4and5.dist
82e36e01fa26480931039ac178ad8e83 *inst/extdata/hg19.genome
75afe0a7c5316fe36c565fd9c77e8b27 *inst/extdata/hg38.genome
8bfdfc78d880056374c42537d696575d *inst/extdata/internal_liftOver_chr4and5.dist
6b069621425e1d115de8c825ecd86620 *inst/extdata/multibranch_liftOver_chr4and5.dist
d7fa277e06a9bdc78f5bcff0af7149a9 *inst/extdata/stem_liftOver_chr4and5.dist
91dab4ee9482c5fc7cf67427b2f4065e *inst/extdata/transcript_list.Rda
ba118a398ee82952ac7476828a201d3c *man/CleanBAMtoBG.Rd
9c72e8f125d3c85e8e454d2b1bc9d801 *man/CleanBEDtoBG.Rd
e47eb9774b6221c76c6a3bcd5fcb0485 *man/ExtractTranscriptomeSequence.Rd
c5fae570fb00454f3fea1caff84487f2 *man/GenomeMappingToChainFile.Rd
dc598a8181c59dc4ac1bc9036986f7c4 *man/assessGrouping.Rd
8849166a3b65496c4e09ea5d50bbb1ec *man/bindingContextDistance.Rd
5281a4bf83212d402c3fe0c4700860d9 *man/bindingContextDistanceCapR.Rd
f7ce6aca25e30f3fbd8f500b6a2cafc9 *man/getChainChrSize.Rd
62511020c3e5f82f2a73d32322b1048e *man/get_outfiles.Rd
6a8dc91f9a51a4dfacd4b03faba9e088 *man/liftOverToExomicBG.Rd
a147f168baff86757ff29a9b27a9672c *man/nearBynding-package.Rd
62e03c04b7f62aa4a4c655234f5bcf7d *man/processCapRout.Rd
25a32efe98adf50769d2e670ee0645a7 *man/runCapR.Rd
0ff968ed156a9cfc43a880ecb74a73c5 *man/runStereogene.Rd
a830e41a3d4e44455eb490fb02fe23ec *man/runStereogeneOnCapR.Rd
50badb61528c391a7185594e7426cf4e *man/symmetryCapR.Rd
e625a8b9ca060b0b3e70603ff0cdce23 *man/symmetryContext.Rd
dfe5cd5c08f918c0518fb3fa0d02f0f9 *man/visualizeCapRStereogene.Rd
345a647551c4aabbf397e6547f87fc58 *man/visualizeStereogene.Rd
03c2d1fcc11315d7e103eda9aa5c9f83 *man/write_config.Rd
8620c50665362e05c01d740be7546186 *man/write_fasta.Rd
af0792664c044f5ee745312fa815dcfb *vignettes/all_contexts_heatmap.jpeg
c1046730924f5fd22d8e052520f0a7a4 *vignettes/all_contexts_line.pdf
6c14d3f68c7d0733bd6cbb64bb80da1f *vignettes/chr4and5_sorted.bedGraph
80c1debda56a3692ad5c95eebf6a39c9 *vignettes/nearBynding.Rmd
e5106872445b37a35645605fbde3c8cc *vignettes/stem_heatmap.jpeg
233b4e05dc679a77958f766eded02463 *vignettes/stem_line.pdf
