ca26b23447fbd85b36394a47d37579c3 *DESCRIPTION
93162dc5c3a9c0b8dad49b3edf809bb1 *NAMESPACE
72ecd186ff9413b48ea2929bb815ed34 *NEWS
a77224ca09ce0fb319515959ba31afa1 *R/DocumentData.R
a8a8055a91790049b2561933d9f91422 *R/GenomicInteractions-class.R
579b6859e0f251818df1ed99e43a7199 *R/GenomicInteractions-package.R
e09008feb75634da51f7672a5f66d0d7 *R/InteractionTrack-class.R
2e2bb304a355d7bca7614fd03d5274a5 *R/annotators.R
06c0fe3720dfac2af62e2922639a99dc *R/calculateDistances.R
1ea5887e7ca377acc15ab775a06ccdff *R/export.R
44e63917fbd70946299213d790b103df *R/export.igraph.R
62ca53205c789a1989d5a4172e42d8f3 *R/getters.R
b5b5a2eacda8d8c159abc18b1d035078 *R/helpers.R
247a7786f69b74aad192da14cc422269 *R/import.R
16c070eeb355ab5c37f42a1fa256ccfb *R/library.R
8cd79bfc4cd5b9a9fe84feb8134182aa *R/plotSummaryStats.R
367fe9948c8159c9ce40a604706b2779 *R/processing.R
070b5ce74d3c39c878c23a5e9cfe3984 *R/setters.R
4156e2db04db5f506d40c170e7a02648 *R/subsetting.R
2506b1241abdf5bbe66d2e3a8725ccb5 *R/summarise_annotations.r
00fa841bd9e4419969c5dc3c971848c0 *R/viewPoints.R
2c670a64e4b87686573aef9b894ef973 *README.md
17c1ee28c3b28fd03381733809e33784 *build/vignette.rds
16e0688115e41fc92394a02831774fc1 *data/hg19.refseq.transcripts.rda
d976d748baf9338534b53095b4433f0f *data/hic_example_data.rda
c3904dc013328074f1a5c5ae17ea5dc2 *data/mm9_refseq_promoters.rda
5235469e94c5954179751fdd3259e40f *data/thymus_enhancers.rda
a345767320ea362a3c159e425679ad5d *inst/CITATION
c3c4c2f5131269e7792aac5a25b3a6d9 *inst/doc/chiapet_vignette.R
e34c12f71d40c09740e5d6babe9dd039 *inst/doc/chiapet_vignette.html
d0416f72a012ca734a7171f6838caf66 *inst/doc/chiapet_vignette.rmd
099a87b3adb1c4d21aa9497fe59ed24c *inst/doc/hic_vignette.R
a27415a65a53e55897ac0c2ee5ec9f52 *inst/doc/hic_vignette.Rmd
201b52e14ea79a8d7aaf97412a812960 *inst/doc/hic_vignette.html
8f4732d26550d64a9dee4252097063a1 *inst/extdata/Seitan2013_WT_100kb_interactions.txt
adc8c65e7510394df1e46053c58796db *inst/extdata/k562.rep1.cluster.pet3+.txt
d2462c11035605c6be41f8876debc607 *man/GInteractions-subsetByFeatures-methods.Rd
ae5bd761b79283d89ccb34d886cdb709 *man/GenomicInteractions-class.Rd
326ecd6cb042979bd9a5c4be3267cb38 *man/GenomicInteractions-package.Rd
662386448c1e594f4df3b27f90c7c1a4 *man/GenomicInteractions.Rd
be82ee0e966ab4c4c93361837cc6f074 *man/InteractionHelpers.Rd
1d33c1c023b08d4f3c52e1b4765e2b40 *man/InteractionTrack-class.Rd
7b8431d88a9fc93d65d82eec0d3d052b *man/InteractionTrack.Rd
f061980bbf69f25078e53b049a72b90c *man/annotateInteractions.Rd
b6d460fbd42562b305b366b580b85122 *man/annotateRegions.Rd
53c620d9817acfccc19e7c5d86187a4d *man/asBED-GInteractions-method.Rd
752e112da3b5bc0226a1de2e21303bb0 *man/availableDisplayPars.Rd
bb7914dd3203fd07b6a4cd6da5b7f460 *man/calculateDistances.Rd
e9f1b2b360475b6c02f09fa2e80ffe1d *man/categoriseInteractions.Rd
c5a52b62ef974ea7bee17c63552472ea *man/countsBetweenAnchors-methods.Rd
8bb4a97566bc4b61017d6231e577cd74 *man/dot-importHicLib.Rd
a5a2ebce141db73c3546100ff0e2edc5 *man/dot-importHomer.Rd
6793c928c8ae037a768a1a1964ed3797 *man/dot-processChiapetName.Rd
f6d3fba2615f37d4d9bc15649b9bee54 *man/dot-readBam.Rd
81e5083967b826595ef01afbda0e2977 *man/dot-readTwoBams.Rd
1feded1307dd7e0d4ad3165087d926b0 *man/dot-validateInput.Rd
1f24525dcbf5206a91f1837656b44d95 *man/export.bed12.Rd
456b657b1e9856ad561923bae0b7d534 *man/export.bedpe.Rd
73c75ae749ea873555840026a52bc6a6 *man/export.chiasig.Rd
7e7f2830cab4c466fcd4d83ba106e50f *man/export.igraph.Rd
801ac1697107d0f6704bae89e39f70b0 *man/get_binom_ligation_threshold.Rd
12be2a05eee26d9c945dd134a2927b03 *man/get_self_ligation_threshold.Rd
3974b1942a25ab9b0cb733a0da983185 *man/getters.Rd
626de40f1bc8ecd18c846764db6eaa1d *man/hg19.refseq.transcripts.Rd
6e818440a418b458fa9c7ed1647bfbe4 *man/hic_example_data.Rd
2d28411226d01de71716fa3ad93481a0 *man/makeGenomicInteractionsFromFile.Rd
6796b2bcecdee2ee36cdb6c87172b8c4 *man/mm9_refseq_promoters.Rd
3e211cca38654ceb362c56ba4d984dfa *man/plotAvgViewpoint.Rd
47b91507834a487c8b1a2890a6ae192b *man/plotCisTrans.Rd
300531fe7dfc0916229446634bfc5ef3 *man/plotCounts.Rd
6442c5f5b83aa58836d03d5bf960968d *man/plotDists.Rd
de926d9e54fe7b30cb38ae5a1fa14673 *man/plotInteractionAnnotations.Rd
f03de110a2831059197a1382d3e488db *man/plotSummaryStats.Rd
d4546c67020220c7f724f2364d30c3b8 *man/plotViewpoint.Rd
5672a3c236b8e8499a17b02de0592262 *man/removeDups.Rd
75e24f40fcc7a04a38dbde12acac1f0b *man/resetAnnotations.Rd
c016bff709481f89aa8b3991e7b0cb7a *man/sameStrand.Rd
812eb0f39040b6464fdf44ce05370b4b *man/setters.Rd
639a4bee68763e362dcf91b955ef0742 *man/sum-GInteractions-method.Rd
39b6181c8d3ccfa37ea888355ef6ada5 *man/summariseByFeaturePairs.Rd
6881ece6edecc073ef316ba46f9fb666 *man/summariseByFeatures.Rd
6b038ffee0525ba1a8b07c936026a45b *man/thymus_enh.Rd
e71afec06469b2f2bbfcd9e5919643db *man/updateObject-GenomicInteractions-method.Rd
677cfa88afaf24112860c8c5b93aeddb *man/viewPoint.Rd
d24261a5a38ac0aa3703519b63ee5d3a *tests/testthat.R
d61623d73debea8fd9fd6e8840489e3c *tests/testthat/test_annotation.R
6b16e74656b0c4018e9baf96a7a03be7 *tests/testthat/test_getters.R
9d6d90de601e36c431fa2ec1acb25d6e *tests/testthat/test_import.R
1ba7f372590aaf38173f51dea2af3460 *tests/testthat/test_interactiontrack.R
ebaa196c07c94fadc0efdb1278a46be8 *tests/testthat/test_summarystats.R
8f94246432a85577c0946b3497fd0b7b *tests/testthat/test_valid.R
0899efa7f235fd8c751244a3c462da83 *tests/testthat/test_viewpoint.R
d0416f72a012ca734a7171f6838caf66 *vignettes/chiapet_vignette.rmd
a27415a65a53e55897ac0c2ee5ec9f52 *vignettes/hic_vignette.Rmd
