OpenScientificCodeRegistry/Database
Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.
05.6k
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/caochch/ric2structure",4 "url": "https://github.com/caochch/RIC2Structure",5 "host": "github.com",6 "commit": "a200b406c96667e4259b44b96fd471c2efbf26df",7 "license": "GPL-3.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "1.Loop_by_HiCCUPS/0.supple_slidingWindows.pl",13 "sha256": "ffd22177c1e9197a0f2aece29268a155df731a41c8d3831ad152d022fa06ffda",14 "language": "Perl",15 "lines": 14,16 "truncated": false,17 "block": 17,18 "row": 1676519 },20 {21 "path": "1.Loop_by_HiCCUPS/1.multiply_factor.pl",22 "sha256": "3de9585d7e5955cdfc34688573fc494855af1abc3a28a6809ad46c7c94fdebe5",23 "language": "Perl",24 "lines": 24,25 "truncated": false,26 "block": 17,27 "row": 1676728 },29 {30 "path": "1.Loop_by_HiCCUPS/2.recover_factorEffect_for_pixels.pl",31 "sha256": "e99ae854bf68944f358cf233435a2a7078abebdad92e2391a34dd744bf2358a3",32 "language": "Perl",33 "lines": 31,34 "truncated": false,35 "block": 17,36 "row": 1678537 },38 {39 "path": "1.Loop_by_HiCCUPS/3.recover_factorEffect_for_loops.pl",40 "sha256": "ed7415d20f29c5e2860cf078b6d31271a6c0af802e87c8a4e8b3f43aba677c7c",41 "language": "Perl",42 "lines": 45,43 "truncated": false,44 "block": 17,45 "row": 1680846 },47 {48 "path": "1.Loop_by_HiCCUPS/4.call_loops_by_cluster_pixels.pl",49 "sha256": "1ef5310cfd78c0c1bc84cff0a71498e7ad94f1c7c6289280e2373f2233dc3d8e",50 "language": "Perl",51 "lines": 42,52 "truncated": false,53 "block": 17,54 "row": 1680955 },56 {57 "path": "1.Loop_by_HiCCUPS/5.format_as_region_loops.pl",58 "sha256": "4fcc5838c94f8c11f42bd054d1dcd933cdde762ab545a222d49056f2a0199978",59 "language": "Perl",60 "lines": 30,61 "truncated": false,62 "block": 17,63 "row": 1677564 },65 {66 "path": "1.Loop_by_HiCCUPS/clustering_bridge_SaveMemory_fast.pl",67 "sha256": "75b45f14081c2613e7f4a07dd0ffa8fc9924e73578c7b21be73f08d747b5a575",68 "language": "Perl",69 "lines": 131,70 "truncated": false,71 "block": 17,72 "row": 1689173 },74 {75 "path": "1.Loop_by_HiCCUPS/format_hic_to_matrix.pl",76 "sha256": "b514acf6976084acec3686721f6c584e2da9e5d300ccc438bd1169e758667fd7",77 "language": "Perl",78 "lines": 44,79 "truncated": false,80 "block": 17,81 "row": 1678882 },83 {84 "path": "2.Loop_by_VCsqrt/1.calculate_VCsqrt_for_eachPixel.pl",85 "sha256": "8ee8dc828c6e1f808bff7f2e5e5cbaf400e833fbae5d1c2b6488250b863529f4",86 "language": "Perl",87 "lines": 95,88 "truncated": false,89 "block": 17,90 "row": 1685291 },92 {93 "path": "2.Loop_by_VCsqrt/2.compare_with_juicebox.pl",94 "sha256": "660b63a67b0b55949baeb703d01324e43ea00d87f8cfa4a73cd501e5a4ab803d",95 "language": "Perl",96 "lines": 32,97 "truncated": false,98 "block": 17,99 "row": 16787100 },101 {102 "path": "2.Loop_by_VCsqrt/3.select_enriched_pixels.pl",103 "sha256": "5c5530c4d29571bb98dd8e20dba1f642aaf708148e500cd47a04076b4cf41e92",104 "language": "Perl",105 "lines": 32,106 "truncated": false,107 "block": 17,108 "row": 16789109 },110 {111 "path": "2.Loop_by_VCsqrt/4.call_loops_by_cluster_pixels.pl",112 "sha256": "8bfa9b9227d08c8308bd2b6242eaa070cdb1d69aee0b6c5f084dbb3d5e28a76e",113 "language": "Perl",114 "lines": 45,115 "truncated": false,116 "block": 17,117 "row": 16816118 },119 {120 "path": "2.Loop_by_VCsqrt/5.format_as_region_loops.pl",121 "sha256": "92023af89db561c3a42e2eea583a80bc0f479a8371a11010eadad4b51398894e",122 "language": "Perl",123 "lines": 36,124 "truncated": false,125 "block": 17,126 "row": 16779127 },128 {129 "path": "2.Loop_by_VCsqrt/6.score_each_loops.pl",130 "sha256": "377f73ba22943ec282978aa1ed69bd6af57cfb866ccbcc99e689bb2913e06ef3",131 "language": "Perl",132 "lines": 217,133 "truncated": false,134 "block": 17,135 "row": 16928136 },137 {138 "path": "2.Loop_by_VCsqrt/6.score_each_loops.v4.pl",139 "sha256": "d073f29ef39d16fdc32f265c884f0e41c46c615bb50751885341d69dea782b9b",140 "language": "Perl",141 "lines": 156,142 "truncated": false,143 "block": 17,144 "row": 16902145 },146 {147 "path": "2.Loop_by_VCsqrt/7.format_as_region_beds.pl",148 "sha256": "58afe123130a72ca4cd4861e95e81bb65d3c1f7152da497a6466d386bb6ea7c6",149 "language": "Perl",150 "lines": 24,151 "truncated": false,152 "block": 17,153 "row": 16768154 },155 {156 "path": "2.Loop_by_VCsqrt/clustering_bridge_SaveMemory_fast.pl",157 "sha256": "75b45f14081c2613e7f4a07dd0ffa8fc9924e73578c7b21be73f08d747b5a575",158 "language": "Perl",159 "lines": 131,160 "truncated": false,161 "block": 17,162 "row": 16891163 },164 {165 "path": "2.Loop_by_VCsqrt/meta_run_step6.pl",166 "sha256": "56176c9facfb30cebd67511f4f6bc6a199ffb9a0e7bf4c7fc623d4e5e92d7f21",167 "language": "Perl",168 "lines": 47,169 "truncated": false,170 "block": 17,171 "row": 16815172 },173 {174 "path": "2.Loop_by_VCsqrt/super_run.pl",175 "sha256": "f82972cb5fd5fff8c0048f032f99747832ced75672c134017c0b724cc47f39fd",176 "language": "Perl",177 "lines": 19,178 "truncated": false,179 "block": 17,180 "row": 16837181 },182 {183 "path": "3a.predict_local_phase1_Score0.05/0.Rscript_ttest.r",184 "sha256": "6078e21b84f014f31fc1ba240ef0437860ef131de3c88e6ffa0dcb23b0d3ff86",185 "language": "R",186 "lines": 8,187 "truncated": false,188 "block": 18,189 "row": 6018190 },191 {192 "path": "3a.predict_local_phase1_Score0.05/1.Heuristics_predict.useRNAstructure.v8.pl",193 "sha256": "787e10831aaf007c10c2a3c2a61e16fe717e0d2ca00af51d215b06a97efa7f05",194 "language": "Perl",195 "lines": 843,196 "truncated": false,197 "block": 17,198 "row": 17038199 },200 {201 "path": "3a.predict_local_phase1_Score0.05/run.sh",202 "sha256": "21438465dd86a684136cf05186d28417fbdf9bbc851f209bf827a9b3a972111e",203 "language": "Shell",204 "lines": 2,205 "truncated": false,206 "block": 18,207 "row": 8823208 },209 {210 "path": "3b.predict_local_phase1_Score0.03/0.Rscript_ttest.r",211 "sha256": "6078e21b84f014f31fc1ba240ef0437860ef131de3c88e6ffa0dcb23b0d3ff86",212 "language": "R",213 "lines": 8,214 "truncated": false,215 "block": 18,216 "row": 6018217 },218 {219 "path": "3b.predict_local_phase1_Score0.03/1.Heuristics_predict.useRNAstructure.contain_input_Constraints.pl",220 "sha256": "09fe1607556a9b6b79389d2522480c478fe01bae7d678813ed48849561cdb318",221 "language": "Perl",222 "lines": 857,223 "truncated": false,224 "block": 17,225 "row": 17041226 },227 {228 "path": "3b.predict_local_phase1_Score0.03/run.sh",229 "sha256": "52b3638e29c2fbccae8e52d117c3c1f2b4e78a2cd5b8c2c96a313b13850dee6d",230 "language": "Shell",231 "lines": 4,232 "truncated": false,233 "block": 18,234 "row": 8920235 },236 {237 "path": "5.fill_Localblanks_phase3_useb/0.Rscript_ttest.r",238 "sha256": "6078e21b84f014f31fc1ba240ef0437860ef131de3c88e6ffa0dcb23b0d3ff86",239 "language": "R",240 "lines": 8,241 "truncated": false,242 "block": 18,243 "row": 6018244 },245 {246 "path": "5.fill_Localblanks_phase3_useb/0.creat_bedpe_from_region.pl",247 "sha256": "6ec6a647c42fca3bf388c3e24ef80022d5667a725cea02c2cf5fa1330d733bfe",248 "language": "Perl",249 "lines": 16,250 "truncated": false,251 "block": 17,252 "row": 16754253 },254 {255 "path": "5.fill_Localblanks_phase3_useb/1.fill_local_blanks.useRNAstructure.v1.pl",256 "sha256": "4a9ff0592430aac8377b985af4bfcd553101c45635d42cccc80b5511ba16428c",257 "language": "Perl",258 "lines": 590,259 "truncated": false,260 "block": 17,261 "row": 17023262 },263 {264 "path": "5.fill_Localblanks_phase3_useb/creat_resolved_region_from_CON.pl",265 "sha256": "56efd460f9e2adcd81491671a8649015f51a6c945ffdd8e3f80af7d798c05874",266 "language": "Perl",267 "lines": 64,268 "truncated": false,269 "block": 17,270 "row": 16851271 },272 {273 "path": "5.fill_Localblanks_phase3_useb/extract_len_and_pvalue.pl",274 "sha256": "8b8bf343237532ba57f307f97731b6ecf9440ac05f2c748f36df3b739e065dff",275 "language": "Perl",276 "lines": 21,277 "truncated": false,278 "block": 17,279 "row": 16758280 },281 {282 "path": "5.fill_Localblanks_phase3_useb/work.sh",283 "sha256": "53ee23a05fa3237a6c924841a482ecb74da4a25f2da902c8b820cbbbe1d0e7ef",284 "language": "Shell",285 "lines": 4,286 "truncated": false,287 "block": 18,288 "row": 8939289 },290 {291 "path": "6.fill_blanks_phase3_useb/0.Rscript_ttest.r",292 "sha256": "6078e21b84f014f31fc1ba240ef0437860ef131de3c88e6ffa0dcb23b0d3ff86",293 "language": "R",294 "lines": 8,295 "truncated": false,296 "block": 18,297 "row": 6018298 },299 {300 "path": "6.fill_blanks_phase3_useb/1.fill_blanks.useRNAstructure.v3.pl",301 "sha256": "eb71112fc795ea97429500b955f2f203142ce06ff0f88e1f06fa568cebfa9d94",302 "language": "Perl",303 "lines": 788,304 "truncated": false,305 "block": 17,306 "row": 17042307 },308 {309 "path": "6.fill_blanks_phase3_useb/c1.check_paired_nucleotide.pl",310 "sha256": "c00d41ec12905d9d230955c1c084c114fbdc8b3efc0a71e33fdd82ec7e5a5892",311 "language": "Perl",312 "lines": 34,313 "truncated": false,314 "block": 17,315 "row": 16794316 },317 {318 "path": "6.fill_blanks_phase3_useb/run.sh",319 "sha256": "af270411ecc7986fffd9e9e016e551146dd2a12325aa30f884ede9d7338e3ae4",320 "language": "Shell",321 "lines": 4,322 "truncated": false,323 "block": 18,324 "row": 8792325 },326 {327 "path": "LICENSE",328 "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",329 "language": "License",330 "lines": 674,331 "truncated": false,332 "block": 1,333 "row": 2235334 },335 {336 "path": "README.md",337 "sha256": "57ffdda9ef232dc84ae0c2c57dc9ea9371873e1188e08875bdb714e19f6ffbd6",338 "language": "Text",339 "lines": 7,340 "truncated": false,341 "block": 18,342 "row": 10426343 },344 {345 "path": "z2.split_domains/7.format_as_region_beds.pl",346 "sha256": "58afe123130a72ca4cd4861e95e81bb65d3c1f7152da497a6466d386bb6ea7c6",347 "language": "Perl",348 "lines": 24,349 "truncated": false,350 "block": 17,351 "row": 16768352 },353 {354 "path": "z2.split_domains/run.sh",355 "sha256": "65baaa75004c7b1e631b5088c88fbcf93ec0282616c3f1973b74600963264ccc",356 "language": "Shell",357 "lines": 1,358 "truncated": false,359 "block": 18,360 "row": 8657361 },362 {363 "path": "z2.split_domains/split_domain.v1.pl",364 "sha256": "671b517ef568d000cd071e095fb7a181e53209c874104d3bc9198f25dee9e0bd",365 "language": "Perl",366 "lines": 176,367 "truncated": false,368 "block": 17,369 "row": 16915370 }371 ]372}