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/adigioacchino/menb_snakemake",4 "url": "https://github.com/adigioacchino/MENB_snakemake",5 "host": "github.com",6 "commit": "28bcc9a3cb9c970b7e927ad351d5e4af92a2a939",7 "license": "MPL-2.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "1f256ecad192880510e84ad60474eab7589218784b9a50bc7ceee34c2b91f1d5",14 "language": "License",15 "lines": 373,16 "truncated": false,17 "block": 6,18 "row": 209019 },20 {21 "path": "MaxEntNucleotideBiases/src/MENB_Gauge.jl",22 "sha256": "5835043adf9714959bed46d868f560716c37ffd0a399aec638c00d1917ec01ff",23 "language": "Julia",24 "lines": 55,25 "truncated": false,26 "block": 22,27 "row": 1231228 },29 {30 "path": "MaxEntNucleotideBiases/src/MENB_InferModel.jl",31 "sha256": "af6e9f0fc6b56035a10da5bedb371d09bd0c15ece85784c1640a34e758a0884c",32 "language": "Julia",33 "lines": 194,34 "truncated": false,35 "block": 22,36 "row": 1237237 },38 {39 "path": "MaxEntNucleotideBiases/src/MENB_PartitionFunction.jl",40 "sha256": "5c6c38a76fb0b1e2bcb8b1da37578b34b72aaf02c23b9d6a55ebbe018aa82b43",41 "language": "Julia",42 "lines": 121,43 "truncated": false,44 "block": 22,45 "row": 1233846 },47 {48 "path": "MaxEntNucleotideBiases/src/MENB_Utils.jl",49 "sha256": "6d4828be80e385d0caa61f9ef680de377800da0701e43590fd31f93836ace643",50 "language": "Julia",51 "lines": 200,52 "truncated": false,53 "block": 22,54 "row": 1236355 },56 {57 "path": "MaxEntNucleotideBiases/src/MaxEntNucleotideBiases.jl",58 "sha256": "6731888fbef55c0c00b3881f2706a4f08e4ef5a0cf3d2300b0828a275e990bc9",59 "language": "Julia",60 "lines": 81,61 "truncated": false,62 "block": 22,63 "row": 1231564 },65 {66 "path": "MaxEntNucleotideBiases/test/runtests.jl",67 "sha256": "a3d2ccbdea32dac3e19a9bb75981bf6ef0656c5074a03b4944ad0479694e6577",68 "language": "Julia",69 "lines": 203,70 "truncated": false,71 "block": 22,72 "row": 1238873 },74 {75 "path": "README.md",76 "sha256": "17d4a491b41229a8162c9e30a82c3bab856c050c9c1b938911159413a70fa16a",77 "language": "Text",78 "lines": 18,79 "truncated": false,80 "block": 24,81 "row": 50182 },83 {84 "path": "computations/workflow/notebooks/figures/fig_classification_performances/fig_performance.jl",85 "sha256": "8e9172d7bb92977cb3ee70a9d9c1fa43e5e200d61ab5b3a7b2abe81243795973",86 "language": "Julia",87 "lines": 2094,88 "truncated": false,89 "block": 22,90 "row": 1242191 },92 {93 "path": "computations/workflow/notebooks/figures/fig_evolution/fig_evolution.jl",94 "sha256": "175d03a092b9a5f58519bfce0b31ea920c25d8403cafc1bd3aea0791e3bab362",95 "language": "Julia",96 "lines": 2086,97 "truncated": false,98 "block": 22,99 "row": 12419100 },101 {102 "path": "computations/workflow/notebooks/figures/fig_expected_values/fig_expected_values.jl",103 "sha256": "e92ab1f47a8c966bbd5bec13bca3656cac1ea725dce508a823583b5ba3dbe44a",104 "language": "Julia",105 "lines": 2019,106 "truncated": false,107 "block": 22,108 "row": 12417109 },110 {111 "path": "computations/workflow/notebooks/figures/fig_interpretation/fig_interpretation_H1N1.jl",112 "sha256": "f6367f4c026541a663fb3a57aee5812e7c0febd9b2d8262604ad2698511f3889",113 "language": "Julia",114 "lines": 2032,115 "truncated": false,116 "block": 22,117 "row": 12418118 },119 {120 "path": "computations/workflow/notebooks/figures/fig_sequence_generation/change_nt_composition.jl",121 "sha256": "9870a7d9f0e83b247460b99dbbee262c16f9081b59a59b9e730df44f2a0008e8",122 "language": "Julia",123 "lines": 1965,124 "truncated": false,125 "block": 22,126 "row": 12414127 },128 {129 "path": "computations/workflow/notebooks/figures/suppl_figs/H1N1_force_reldiffs.jl",130 "sha256": "206be186bda5a4c4c490d4b297b7e085436e24c622bc9365c9871dda43a5cc3e",131 "language": "Julia",132 "lines": 1797,133 "truncated": false,134 "block": 22,135 "row": 12409136 },137 {138 "path": "computations/workflow/notebooks/figures/suppl_figs/KL_table.jl",139 "sha256": "43ad9fc8c3b30e726549d6480c6fde850cf8cb530fa0ea1e743888512a6caaf6",140 "language": "Julia",141 "lines": 1708,142 "truncated": false,143 "block": 22,144 "row": 12406145 },146 {147 "path": "computations/workflow/notebooks/figures/suppl_figs/allfreqsdiffs.jl",148 "sha256": "7e0b360af7890f21078ada15d892b20bfda94a0cd596dccbd6b225b85b61134b",149 "language": "Julia",150 "lines": 1691,151 "truncated": false,152 "block": 22,153 "row": 12407154 },155 {156 "path": "computations/workflow/notebooks/figures/suppl_figs/attribution_plots.jl",157 "sha256": "b17fb704f84a69871a2d7e93052c51e737ee9d9de5b26b22aad461618451b6f0",158 "language": "Julia",159 "lines": 1759,160 "truncated": false,161 "block": 22,162 "row": 12408163 },164 {165 "path": "computations/workflow/notebooks/figures/suppl_figs/attributions_nonsymmetrized_KL.jl",166 "sha256": "8dd310bc6aef5e0eff03e30318d15fc9f6951e97e234a32626d606e767cd5579",167 "language": "Julia",168 "lines": 1959,169 "truncated": false,170 "block": 22,171 "row": 12413172 },173 {174 "path": "computations/workflow/notebooks/figures/suppl_figs/compare_nt_compositions_synthetic.jl",175 "sha256": "5dce9365490d11d07683d5f2b2c6457354c1055ec083a8353e2ece284f5b9697",176 "language": "Julia",177 "lines": 1967,178 "truncated": false,179 "block": 22,180 "row": 12415181 },182 {183 "path": "computations/workflow/notebooks/figures/suppl_figs/evolution_nts_CpG.jl",184 "sha256": "937d09d6f7f473ddd9be73ee5adb5e4b455212c6621f7db71949040b231faecc",185 "language": "Julia",186 "lines": 2126,187 "truncated": false,188 "block": 22,189 "row": 12420190 },191 {192 "path": "computations/workflow/notebooks/figures/suppl_figs/expected_values_training.jl",193 "sha256": "7887283fcdaa6b8776beeb66bdf0f359694554ebe9628758dce29759f1913a9a",194 "language": "Julia",195 "lines": 1921,196 "truncated": false,197 "block": 22,198 "row": 12412199 },200 {201 "path": "computations/workflow/notebooks/figures/suppl_figs/force_plots.jl",202 "sha256": "23baa8d6de3e8bf8a9ea5f03f78eb6bdac6e6c6c0648fbfab774584d9db4c553",203 "language": "Julia",204 "lines": 1685,205 "truncated": false,206 "block": 22,207 "row": 12405208 },209 {210 "path": "computations/workflow/notebooks/figures/suppl_figs/interpretation_SARS2.jl",211 "sha256": "263ddf2b9bb668bc1b409b19f4b8f5083ac35bbe66fdb39f731151a3356d9790",212 "language": "Julia",213 "lines": 2031,214 "truncated": false,215 "block": 22,216 "row": 12416217 },218 {219 "path": "computations/workflow/notebooks/figures/suppl_figs/interpretation_orthomyxo.jl",220 "sha256": "fd5f8b623f3fe3395c4d0468eba00af27b4b788942822cd922fb3367b27d84ac",221 "language": "Julia",222 "lines": 1899,223 "truncated": false,224 "block": 22,225 "row": 12411226 },227 {228 "path": "computations/workflow/scripts/VIDHOP_prepare_seqs_hosts.jl",229 "sha256": "cca744847081ab9ba10fad2676690652fe916602585641c6d0bc28f57b8c5e8f",230 "language": "Julia",231 "lines": 59,232 "truncated": false,233 "block": 22,234 "row": 12307235 },236 {237 "path": "computations/workflow/scripts/fit_nucleotide_model_full.jl",238 "sha256": "eb969f3aa94c635a0d9e7f7ca8825809d94e52b20a6fa0ef521cb76cc191a845",239 "language": "Julia",240 "lines": 23,241 "truncated": false,242 "block": 22,243 "row": 12293244 },245 {246 "path": "computations/workflow/scripts/fit_nucleotide_model_half.jl",247 "sha256": "77a135d700003524acd97ee04106620ad4bc7070f085cef4815abdd7ff233191",248 "language": "Julia",249 "lines": 24,250 "truncated": false,251 "block": 22,252 "row": 12294253 },254 {255 "path": "computations/workflow/scripts/infer_hosts.jl",256 "sha256": "8f6e16ecb3e4ef2b9f9458dbc015b36380e6cad7d8a7f7ff52aec2802bf15c58",257 "language": "Julia",258 "lines": 117,259 "truncated": false,260 "block": 22,261 "row": 12349262 },263 {264 "path": "computations/workflow/scripts/mergefamilies_training_test.jl",265 "sha256": "e2a566b7b40741ee4d294efb878fd659fa04e1aabb75f3668e2923f44e462442",266 "language": "Julia",267 "lines": 41,268 "truncated": false,269 "block": 22,270 "row": 12303271 },272 {273 "path": "computations/workflow/scripts/split_training_test.jl",274 "sha256": "dbe05e3ab8b72d1aa7f968f407379801656c5ad2b25e5b7b494ac810d25cf8ee",275 "language": "Julia",276 "lines": 39,277 "truncated": false,278 "block": 22,279 "row": 12298280 }281 ]282}