86d9408b57680e485eb193e9bfb70390 *DESCRIPTION
0d7e1cbd28fee87bcdcee520234aa92a *NAMESPACE
ed5e8a052a8f57bd0abd34bfa391f755 *NEWS.md
20ad5330d0367cae07f339f935460e95 *R/RcppExports.R
9c50e64bd810370281b10769c5179141 *R/data.R
171d6ed6d403877e05c468cf04f1b8f0 *R/params.R
c4348b02bc53896351b04e129141a13d *R/shaman-package.r
77ab6c04678cc29371ec9e8c183a0163 *R/shaman.R
36e4cf6848067305ca58c351028a6f75 *R/shaman_conf.R
85cc7a72e19a13419c34e0b5b5c91f33 *R/shaman_feature_grid.R
a51942ed06e47cc89311c5d87db29508 *R/shaman_plot_map.R
24a3d23c6fe9ee62b9e18f6c04560dbe *R/zzz.R
81da78a283d85e479584e86d7cae8b30 *README.md
aa5e5a2cbfaea3d9b6cdbe378ac48cee *build/partial.rdb
fdc2d372ae539f1463b1439b785d55fa *build/vignette.rds
f568692d70fe2c13691ddf5c1fdff5fe *data/ctcf_forward.rda
b78c89938c7eacd036ed945f668035dc *data/ctcf_reverse.rda
21c45271a7e78472b4c8b870079c0bf2 *inst/CITATION
5d6be5697387ff2d5ad020c8dbc9d152 *inst/config/shaman.conf
d761d6bbec8c7874b9939c92532f9595 *inst/doc/import.R
68a645ed1262254c9f1ae2d6ad381dc9 *inst/doc/import.Rmd
3a42279adf65d20542e75593fd656e1d *inst/doc/import.html
1817f400ad63d0e97c2361495743af1d *inst/doc/shaman-package.Rmd
9f2bcfb9d7588adfae2618838a78b38a *inst/doc/shaman-package.html
b3c497216c61fb01a6a7e13519edd1e2 *inst/extdata/hoxd.tsv.xz
472f7506fd400d9fa5bd58c93687e8a4 *inst/perl/hic_merge_ks.pl
88116d78f851c509721a65008003e45f *man/ctcf_forward.Rd
ac41f7861f8734548f995186bb0adb7c *man/ctcf_reverse.Rd
e109ee72989d0d794842db1b33b75c23 *man/dot-shaman_dump_config.Rd
3520f95ac7e85f636e222fc72c131ca0 *man/dot-shaman_load_config.Rd
4de68163652196932f39bfe4a28f6344 *man/get_param.Rd
8d1a12cfcc354049ba5f6e0ea51860c4 *man/get_param_list.Rd
ed01db45bf3573500c708281cd408fc0 *man/init_params.Rd
60a63c0e9b148c320f3e9ea1e6385e39 *man/shaman-package.Rd
3bbd2634cc4f8c406dc17649e8f12ea9 *man/shaman_generate_feature_grid.Rd
32995b7807655f77e3f0b700ded863dc *man/shaman_get_test_track_db.Rd
d4ce0391441ae8a6a8003564f330cfcf *man/shaman_gplot_map.Rd
42f0186c919d689defa558f713c05f94 *man/shaman_gplot_map_score.Rd
c60a9b7c35f5cae31c2b9dce80608e87 *man/shaman_kk_norm.Rd
b8a66d88f3e614cdd79957ba107e99f3 *man/shaman_plot_feature_grid.Rd
ff2de25bb6492c24c4dcf608052cb07c *man/shaman_plot_map_score_with_annotations.Rd
6b022d9fff328d5d7a3901f9ceb21be2 *man/shaman_plot_tracks_and_annotations.Rd
325aeefcb33ce9c96e07f549a24dfa1c *man/shaman_score_hic_mat.Rd
3ad1063e739a41ee040b3c616e91455c *man/shaman_score_hic_mat_for_track.Rd
91e61812c6f3b46ec60d7c637cc5d793 *man/shaman_score_hic_points.Rd
fb53d1e1173e013851ba16f434acdd9d *man/shaman_score_hic_track.Rd
995898149a0e1402c60d5712aeb636f5 *man/shaman_score_pal.Rd
07b2f79dcba81ed7a47feb4151bf0a01 *man/shaman_shuffle_and_score_hic_mat.Rd
dcb23b51181b3f941aea2a2cd66339e9 *man/shaman_shuffle_hic_mat_for_track.Rd
b32b083269997d75ce605c5077fad7b7 *man/shaman_shuffle_hic_track.Rd
7ddafb8552fd796d683dface73bd194f *src/ContactShuffler.cpp
8dc6c02bbdd239e937d68bd3dd1d6ffd *src/ContactShuffler.h
ca3599ae97e348b581288765711ba026 *src/GenomeGridLog.cpp
970cab8bf03648eedad21f51a4accddf *src/GenomeGridLog.h
842fcdc959bbc41c3933353a409e4833 *src/Makevars
79888636b69d0e714393c797edd99cd9 *src/MathUtils.h
253672bf958cfafa65cca1f9eff783dd *src/Parser.cpp
8ecd475f3a3df90f2c8ed2a372670aaf *src/Parser.h
94d0594c56582ac78b27ac1c86383a41 *src/Random.cpp
e3b10632e6d4423ac5b8d6ae9a8782b1 *src/Random.h
ad724fb45995d5d5bcdd3a08616de319 *src/RcppExports.cpp
2f0f7b8fde357d8a99a67b4cedba35d6 *src/VectorUtils.h
17acc6eccebfde86aa517641be92ceed *src/hic_matrix_shuffler.cpp
4a09499a67a5c2af3746de7dd9ef8507 *src/macro.h
05f9fb053cf821bce322a95505626dad *src/merge_ks.cpp
4513d8386b1190672d86eb3c5c8ecf31 *tests/testthat.R
7a8e7f7c03c54346947869f5177f44c4 *tests/testthat/helper-db.R
9fd1c41ec932b3c074ee169a5f2e2096 *tests/testthat/test-example_db.R
601e187f83ffb3cfe676ecc6465a3887 *tests/testthat/test-knn_ks.R
d7bba8c230cd28288af0aad82d950c27 *tests/testthat/test-mc_failure.R
6c05a183aeafcd76be92a89e34c7a81e *tests/testthat/test-merge_ks.R
db981f963b92e11260fed76b5e8465d9 *tests/testthat/test-score_and_small_input.R
7477cc42aae9fdf321c421185f3cf1ef *tests/testthat/test-score_paths.R
59faa1f43db40d0ab98d28ae8f5c9c87 *tests/testthat/test-sort_uniq.R
68a645ed1262254c9f1ae2d6ad381dc9 *vignettes/import.Rmd
c1df6bb5731274f5dee647bfc004ffbb *vignettes/shaman-package-ctcf-grid-1.png
46c2b89586cb1bbb6ba59c7685191a3f *vignettes/shaman-package-score-map-1.png
1817f400ad63d0e97c2361495743af1d *vignettes/shaman-package.Rmd
