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LICENSE | 644 | 0 | 0 | | | 1.1 KB | 7071e3994397017e5dddcd44e9421ea30e30a6cf5261485742ae429970983758 |
README.md | 644 | 0 | 0 | | | 3.43 KB | 4b20d320b37bbd190fe9d1e78443e2af1ff6e39a4ddebb1050957cadee07ced6 |
Rakefile.rb | 644 | 0 | 0 | | | 1.59 KB | 15baa95bbc351d46e135792076d4ecbb619b144e98e8cf873957ec14ef66874c |
TODO.txt | 644 | 0 | 0 | | | 1.43 KB | ba09c56cc93b2333a04278f6a82c2a482505002943438fa16041b1df7cd28157 |
benchmark/benchmark_helper.rb | 644 | 0 | 0 | | | 200 Bytes | 619aabb0e90b128f59c4748d01083486932aa396335d1b37c8f95e960cd8df60 |
benchmark/similarity_benchmark.rb | 644 | 0 | 0 | | | 2.68 KB | 10f09ae0df6c39e3f7d5b3ef278ecc53ce0d075b18670ec76bb157c988761a33 |
bin/align_motifs | 644 | 0 | 0 | | | 113 Bytes | fa7b4b27ef0e0f256ab2187ea6f4ccd59c2ebd66f86bfeb96410642bcb48f328 |
bin/eval_alignment | 644 | 0 | 0 | | | 117 Bytes | 00573e811487458c855a739971b4900c80bb5a30eac7ccf09aadf534d5adb5ab |
bin/eval_similarity | 644 | 0 | 0 | | | 119 Bytes | 5c93c05a8a3ee7e2533234a85c927aebbf39136ebd3954b8ee8e3b27dc779d36 |
bin/find_pvalue | 644 | 0 | 0 | | | 111 Bytes | aef2c3e19e550eeef6c27f00d4e511b59aaa9c48aa81773439d48ad66c3a04e5 |
bin/find_threshold | 644 | 0 | 0 | | | 117 Bytes | 803b0343a051165968c1967d1a873f90d1d4e489a573fac2573a561f9def101c |
bin/preprocess_collection | 644 | 0 | 0 | | | 131 Bytes | 1d869f1c0af5ef1015dcdb18496a071cdd1e8a1a5ad57167623de902a3d9dcea |
bin/scan_collection | 644 | 0 | 0 | | | 119 Bytes | d343ddb582bef42cf9b0ece135fb8674dbce693a8792c09b5f770ce1a1b333c8 |
lib/macroape.rb | 644 | 0 | 0 | | | 307 Bytes | a3499c5e70f3b47f71a3635c6a2cb805151786abd6453a1a160147fbaf1e420f |
lib/macroape/aligned_pair_intersection.rb | 644 | 0 | 0 | | | 2.76 KB | f93c660cf99245f0e6cd90c1031968250eecd322b74de5e220fb9ebea81bdd1f |
lib/macroape/cli.rb | 644 | 0 | 0 | | | 47 Bytes | 339692f1d9e0adef4e5480ad5fce92c0d754b55279ad112267533dddce3bcfbf |
lib/macroape/cli/align_motifs.rb | 644 | 0 | 0 | | | 1.62 KB | 820afdd8b95b6a16746b12fe4069ea90efd9d7d755a9fde19e5fa3d2a339208a |
lib/macroape/cli/eval_alignment.rb | 644 | 0 | 0 | | | 5.04 KB | d51e787a465e15ee6f8c75929c9ac9d6b929f1fc7094417e7c87dfb9fa8fb1ca |
lib/macroape/cli/eval_similarity.rb | 644 | 0 | 0 | | | 4.46 KB | 1c3eec62ae3bf114d91f17bc7461e568fd7ab714e2cf98e79f6c0e30b49cba32 |
lib/macroape/cli/find_pvalue.rb | 644 | 0 | 0 | | | 3.05 KB | 467df051ce440a009c5c162b0817ffafec604ba7b15a51ffaf29023dd7bafeed |
lib/macroape/cli/find_threshold.rb | 644 | 0 | 0 | | | 2.73 KB | cbb519a1297286830f883b464874fe43d695655d9b4d506e1e61d77fc9f4a3c5 |
lib/macroape/cli/preprocess_collection.rb | 644 | 0 | 0 | | | 6.07 KB | 846d0dfef99329c4a05e1094a9d3bfd24ad7d33888eebd041944b65747f04a52 |
lib/macroape/cli/scan_collection.rb | 644 | 0 | 0 | | | 7.19 KB | 488feb480364f8199166ffcb87ce3a8420ffad79ae9e4e9481408f5aec6f0458 |
lib/macroape/counting.rb | 644 | 0 | 0 | | | 3.6 KB | 9c149b61f27427d68f61ee293255c9ddd762c1ff077c2db8cf1b26359876c9ad |
lib/macroape/pwm_compare.rb | 644 | 0 | 0 | | | 1.28 KB | 37c70457e3c3676114359e793212b51adc175adfe8cd0dfc1b7706e90ce48b41 |
lib/macroape/pwm_compare_aligned.rb | 644 | 0 | 0 | | | 3.61 KB | 6f5e6bc7385133b1d05248923def99c285df65568eff9f890a2126e1d8a19f4c |
lib/macroape/version.rb | 644 | 0 | 0 | | | 43 Bytes | 89877769942e60dc6006a628d41d2b8e848f028dcc49abffd2686b27dfbd5ac6 |
macroape.gemspec | 644 | 0 | 0 | | | 1.16 KB | 5aa874ba5ca5efd5c832797d0e88361cb659f93931537bb3f54327b30462fecb |
spec/count_distribution_spec.rb | 644 | 0 | 0 | | | 2.25 KB | 0e9aaf6724392c350dca20871e8fa5f2c9ab89326acf3a433498ec74fb0ff7f8 |
spec/spec_helper.rb | 644 | 0 | 0 | | | 160 Bytes | 9d2d6144f92b42483f6617a9a00278ed43b0d63a321d9a34647608789b824af1 |
test/align_motifs_test.rb | 644 | 0 | 0 | | | 653 Bytes | 60f73635706c69a1954d1375d74b36fb2a93100bde25e5891b51f305bca667ec |
test/data/AHR_si.pat | 644 | 0 | 0 | | | 722 Bytes | a8304924977c401e63349f6b9af6c6813c405ad5c3030ee6bba6505c3c02ac83 |
test/data/KLF3_f1.pat | 644 | 0 | 0 | | | 1.2 KB | 36e0890feb68597c36b3248ed9065afaafd0a34966b9a0bb4f5dd5affc0715d3 |
test/data/KLF3_f1.pcm | 644 | 0 | 0 | | | 379 Bytes | 25914e2bfd80bdab64e416266590109ff55b1750985d5a86ccf3ab877b29b894 |
test/data/KLF4_f2.pat | 644 | 0 | 0 | | | 803 Bytes | 4008999624df7698e42c4448dcee6f03a5db1a0eeb9ea832affe2d280d5aa6b3 |
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test/data/KLF4_f2_scan_results_all.txt | 644 | 0 | 0 | | | 154 Bytes | 84cea1cc95cbde6f5c3525db19d6a2e4be389a0dcf9bad75a455c814439e1397 |
test/data/KLF4_f2_scan_results_default_cutoff.txt | 644 | 0 | 0 | | | 109 Bytes | 3481d96456de2b045a490096c521d8654b57fce76359b4f137ae0ad8ac7b1251 |
test/data/KLF4_f2_scan_results_precise_mode.txt | 644 | 0 | 0 | | | 157 Bytes | 18d1892f99dd24d8ff5cf56be30234a1abd5d6e09586389054756a33968ff3c6 |
test/data/SP1_f1.pat | 644 | 0 | 0 | | | 881 Bytes | 2176f1666d2fad0be173c6abc13f2a522c0e9fea1f6baa68a8a7c8c0598050bb |
test/data/SP1_f1.pcm | 644 | 0 | 0 | | | 845 Bytes | cba5cc59f78a91f098911bca43318e0976f5d0c07cdb2c7e0751228a661daf12 |
test/data/SP1_f1_revcomp.pat | 644 | 0 | 0 | | | 885 Bytes | c45f8ded088ffd75bb18359af24ad3ba488492a8a3cf616f7b67f4e18cfce8aa |
test/data/SP1_f1_revcomp.pcm | 644 | 0 | 0 | | | 845 Bytes | 6d00d28005d20aa05b6219bc443cd0b56267d58ad427f8c2cc2752f83cade0b7 |
test/data/collection_pcm_without_thresholds.yaml | 644 | 0 | 0 | | | 4.51 KB | 6f7518af4f120267585be15bec7b9cfd00fa2585c1c4053be9709b7190e43890 |
test/data/collection_without_thresholds.yaml | 644 | 0 | 0 | | | 4.78 KB | 539c1723d9e3e577f606441bd4c407cf38edc2eeba16bcda0ee2f660a891707f |
test/data/medium_motif.pat | 644 | 0 | 0 | | | 568 Bytes | 6ecc8260faebc904330968193e2eb9823abacda03285c120d87f8cf5cf433501 |
test/data/short_motif.pat | 644 | 0 | 0 | | | 489 Bytes | 9c1e8a5bc0c95b8e09040224d0b7986ce0770d0bf9b8542b2fbbad5c8c520271 |
test/data/test_collection.yaml | 644 | 0 | 0 | | | 5.46 KB | 3fb5be8548c1c0e261163d4e225eb1ff800373af5833f4f0233ebda5a0005d94 |
test/data/test_collection/GABPA_f1.pat | 644 | 0 | 0 | | | 1.03 KB | b2d9524de0ed018fb67b03ead0de28f389d75bcd83776c3492c38dc45f1e2df7 |
test/data/test_collection/KLF4_f2.pat | 644 | 0 | 0 | | | 790 Bytes | 83f3d3c31909ea396b4ac3bb3c6bee6eea748200e818a080da553913f409f40f |
test/data/test_collection/SP1_f1.pat | 644 | 0 | 0 | | | 881 Bytes | 2176f1666d2fad0be173c6abc13f2a522c0e9fea1f6baa68a8a7c8c0598050bb |
test/data/test_collection_pcm/GABPA_f1.pcm | 644 | 0 | 0 | | | 907 Bytes | 1d724cbaf940aa3b4e6e5765eeb98e960f16b996495c22c73d66444b0b577741 |
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test/data/test_collection_single_file.txt | 644 | 0 | 0 | | | 2.67 KB | 2fbcf7277308a4c23ffb444cb88ff89681a68dc598082503488eff33c28c00fd |
test/data/test_collection_single_file_pcm.txt | 644 | 0 | 0 | | | 2.48 KB | 5ab13c43f1c5f1566275d7b36284e484ef9db2619dd1dd966b97a1eeca591636 |
test/eval_alignment_test.rb | 644 | 0 | 0 | | | 1.88 KB | c2b56249e610dc1a902887ebbeb4593f2d4a6e67fa2c1e84b5778901a1de2111 |
test/eval_similarity_test.rb | 644 | 0 | 0 | | | 2.04 KB | 039d490ae0bbef2c6a7dfec7835a34da9fd6e0d07107a2bc3cbd9ce91b77232a |
test/find_pvalue_test.rb | 644 | 0 | 0 | | | 1.24 KB | f316267f93db6b7df1f518a556bb6e9577f960f7a2cd65a88404d97280dfe6aa |
test/find_threshold_test.rb | 644 | 0 | 0 | | | 1.91 KB | 2bfe6f7f23018c84d1c0d373c1e3828ec268e52ebaf3a5b623425de15892d7f1 |
test/preprocess_collection_test.rb | 644 | 0 | 0 | | | 3.83 KB | 10d929db31a82ee9e63300905289db69128ca519a3b604bf95ab67569937cc33 |
test/scan_collection_test.rb | 644 | 0 | 0 | | | 2.29 KB | b51531e8ab36ddbdcfbcc8c4d24e75b28c1b83941609dbdd61705cb0c0fac743 |
test/test_helper.rb | 644 | 0 | 0 | | | 2.58 KB | 993e1cdbabd9a2004d14657ac8118dc039cc2efa6c2ca751bd51683d40b5bf99 |