@hongmaple0820/med-scale-research-os 0.43.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1104) hide show
  1. package/.scale/mcp-servers.yaml +144 -0
  2. package/.scale/skills.json +830 -0
  3. package/.scale/verification.json +52 -0
  4. package/LICENSE +15 -0
  5. package/README.en.md +156 -0
  6. package/README.md +156 -0
  7. package/dist/adapters/AiderAdapter.d.ts +22 -0
  8. package/dist/adapters/AiderAdapter.js +262 -0
  9. package/dist/adapters/AiderAdapter.js.map +1 -0
  10. package/dist/adapters/AntigravityAdapter.d.ts +4 -0
  11. package/dist/adapters/AntigravityAdapter.js +21 -0
  12. package/dist/adapters/AntigravityAdapter.js.map +1 -0
  13. package/dist/adapters/ClaudeCodeAdapter.d.ts +54 -0
  14. package/dist/adapters/ClaudeCodeAdapter.js +185 -0
  15. package/dist/adapters/ClaudeCodeAdapter.js.map +1 -0
  16. package/dist/adapters/ClineAdapter.d.ts +4 -0
  17. package/dist/adapters/ClineAdapter.js +20 -0
  18. package/dist/adapters/ClineAdapter.js.map +1 -0
  19. package/dist/adapters/CodexAdapter.d.ts +15 -0
  20. package/dist/adapters/CodexAdapter.js +160 -0
  21. package/dist/adapters/CodexAdapter.js.map +1 -0
  22. package/dist/adapters/CursorAdapter.d.ts +14 -0
  23. package/dist/adapters/CursorAdapter.js +171 -0
  24. package/dist/adapters/CursorAdapter.js.map +1 -0
  25. package/dist/adapters/DeepSeekTuiAdapter.d.ts +19 -0
  26. package/dist/adapters/DeepSeekTuiAdapter.js +263 -0
  27. package/dist/adapters/DeepSeekTuiAdapter.js.map +1 -0
  28. package/dist/adapters/DoubaoAdapter.d.ts +14 -0
  29. package/dist/adapters/DoubaoAdapter.js +184 -0
  30. package/dist/adapters/DoubaoAdapter.js.map +1 -0
  31. package/dist/adapters/GeminiAdapter.d.ts +14 -0
  32. package/dist/adapters/GeminiAdapter.js +163 -0
  33. package/dist/adapters/GeminiAdapter.js.map +1 -0
  34. package/dist/adapters/GenericProjectAgentAdapter.d.ts +29 -0
  35. package/dist/adapters/GenericProjectAgentAdapter.js +204 -0
  36. package/dist/adapters/GenericProjectAgentAdapter.js.map +1 -0
  37. package/dist/adapters/HermesAdapter.d.ts +14 -0
  38. package/dist/adapters/HermesAdapter.js +163 -0
  39. package/dist/adapters/HermesAdapter.js.map +1 -0
  40. package/dist/adapters/JCodeAdapter.d.ts +4 -0
  41. package/dist/adapters/JCodeAdapter.js +19 -0
  42. package/dist/adapters/JCodeAdapter.js.map +1 -0
  43. package/dist/adapters/KiloCodeAdapter.d.ts +4 -0
  44. package/dist/adapters/KiloCodeAdapter.js +20 -0
  45. package/dist/adapters/KiloCodeAdapter.js.map +1 -0
  46. package/dist/adapters/KimiAdapter.d.ts +14 -0
  47. package/dist/adapters/KimiAdapter.js +183 -0
  48. package/dist/adapters/KimiAdapter.js.map +1 -0
  49. package/dist/adapters/KiroAdapter.d.ts +14 -0
  50. package/dist/adapters/KiroAdapter.js +180 -0
  51. package/dist/adapters/KiroAdapter.js.map +1 -0
  52. package/dist/adapters/OpenClawAdapter.d.ts +14 -0
  53. package/dist/adapters/OpenClawAdapter.js +163 -0
  54. package/dist/adapters/OpenClawAdapter.js.map +1 -0
  55. package/dist/adapters/OpenCodeAdapter.d.ts +14 -0
  56. package/dist/adapters/OpenCodeAdapter.js +172 -0
  57. package/dist/adapters/OpenCodeAdapter.js.map +1 -0
  58. package/dist/adapters/QCoderAdapter.d.ts +14 -0
  59. package/dist/adapters/QCoderAdapter.js +159 -0
  60. package/dist/adapters/QCoderAdapter.js.map +1 -0
  61. package/dist/adapters/QoderAdapter.d.ts +4 -0
  62. package/dist/adapters/QoderAdapter.js +21 -0
  63. package/dist/adapters/QoderAdapter.js.map +1 -0
  64. package/dist/adapters/TraeAdapter.d.ts +14 -0
  65. package/dist/adapters/TraeAdapter.js +159 -0
  66. package/dist/adapters/TraeAdapter.js.map +1 -0
  67. package/dist/adapters/VSCAdapter.d.ts +14 -0
  68. package/dist/adapters/VSCAdapter.js +159 -0
  69. package/dist/adapters/VSCAdapter.js.map +1 -0
  70. package/dist/adapters/WindsurfAdapter.d.ts +14 -0
  71. package/dist/adapters/WindsurfAdapter.js +185 -0
  72. package/dist/adapters/WindsurfAdapter.js.map +1 -0
  73. package/dist/adapters/WorkBuddyAdapter.d.ts +14 -0
  74. package/dist/adapters/WorkBuddyAdapter.js +159 -0
  75. package/dist/adapters/WorkBuddyAdapter.js.map +1 -0
  76. package/dist/adapters/index.d.ts +32 -0
  77. package/dist/adapters/index.js +87 -0
  78. package/dist/adapters/index.js.map +1 -0
  79. package/dist/agents/AgentChannel.d.ts +43 -0
  80. package/dist/agents/AgentChannel.js +136 -0
  81. package/dist/agents/AgentChannel.js.map +1 -0
  82. package/dist/agents/AgentCoordinator.d.ts +29 -0
  83. package/dist/agents/AgentCoordinator.js +136 -0
  84. package/dist/agents/AgentCoordinator.js.map +1 -0
  85. package/dist/agents/AgentDispatcher.d.ts +24 -0
  86. package/dist/agents/AgentDispatcher.js +112 -0
  87. package/dist/agents/AgentDispatcher.js.map +1 -0
  88. package/dist/agents/AgentManager.d.ts +14 -0
  89. package/dist/agents/AgentManager.js +85 -0
  90. package/dist/agents/AgentManager.js.map +1 -0
  91. package/dist/agents/AgentPool.d.ts +59 -0
  92. package/dist/agents/AgentPool.js +192 -0
  93. package/dist/agents/AgentPool.js.map +1 -0
  94. package/dist/agents/AgentRegistry.d.ts +20 -0
  95. package/dist/agents/AgentRegistry.js +36 -0
  96. package/dist/agents/AgentRegistry.js.map +1 -0
  97. package/dist/agents/AgentSourceLoader.d.ts +73 -0
  98. package/dist/agents/AgentSourceLoader.js +103 -0
  99. package/dist/agents/AgentSourceLoader.js.map +1 -0
  100. package/dist/agents/IAgent.d.ts +53 -0
  101. package/dist/agents/IAgent.js +4 -0
  102. package/dist/agents/IAgent.js.map +1 -0
  103. package/dist/agents/LeadershipPresets.d.ts +16 -0
  104. package/dist/agents/LeadershipPresets.js +152 -0
  105. package/dist/agents/LeadershipPresets.js.map +1 -0
  106. package/dist/agents/definitions/debugger.d.ts +2 -0
  107. package/dist/agents/definitions/debugger.js +6 -0
  108. package/dist/agents/definitions/debugger.js.map +1 -0
  109. package/dist/agents/definitions/doc-writer.d.ts +2 -0
  110. package/dist/agents/definitions/doc-writer.js +6 -0
  111. package/dist/agents/definitions/doc-writer.js.map +1 -0
  112. package/dist/agents/definitions/implementer.d.ts +2 -0
  113. package/dist/agents/definitions/implementer.js +6 -0
  114. package/dist/agents/definitions/implementer.js.map +1 -0
  115. package/dist/agents/definitions/planner.d.ts +2 -0
  116. package/dist/agents/definitions/planner.js +6 -0
  117. package/dist/agents/definitions/planner.js.map +1 -0
  118. package/dist/agents/definitions/researcher.d.ts +2 -0
  119. package/dist/agents/definitions/researcher.js +6 -0
  120. package/dist/agents/definitions/researcher.js.map +1 -0
  121. package/dist/agents/definitions/reviewer.d.ts +2 -0
  122. package/dist/agents/definitions/reviewer.js +6 -0
  123. package/dist/agents/definitions/reviewer.js.map +1 -0
  124. package/dist/agents/definitions/security.d.ts +2 -0
  125. package/dist/agents/definitions/security.js +6 -0
  126. package/dist/agents/definitions/security.js.map +1 -0
  127. package/dist/agents/definitions/tester.d.ts +2 -0
  128. package/dist/agents/definitions/tester.js +6 -0
  129. package/dist/agents/definitions/tester.js.map +1 -0
  130. package/dist/agents/index.d.ts +23 -0
  131. package/dist/agents/index.js +44 -0
  132. package/dist/agents/index.js.map +1 -0
  133. package/dist/agents/profiles.d.ts +26 -0
  134. package/dist/agents/profiles.js +197 -0
  135. package/dist/agents/profiles.js.map +1 -0
  136. package/dist/agents/types.d.ts +262 -0
  137. package/dist/agents/types.js +4 -0
  138. package/dist/agents/types.js.map +1 -0
  139. package/dist/api/cli.d.ts +2 -0
  140. package/dist/api/cli.js +6678 -0
  141. package/dist/api/cli.js.map +1 -0
  142. package/dist/api/doctor.d.ts +83 -0
  143. package/dist/api/doctor.js +982 -0
  144. package/dist/api/doctor.js.map +1 -0
  145. package/dist/api/mcp.d.ts +32 -0
  146. package/dist/api/mcp.js +223 -0
  147. package/dist/api/mcp.js.map +1 -0
  148. package/dist/api/medscale.d.ts +2 -0
  149. package/dist/api/medscale.js +20 -0
  150. package/dist/api/medscale.js.map +1 -0
  151. package/dist/api/quickstart.d.ts +86 -0
  152. package/dist/api/quickstart.js +291 -0
  153. package/dist/api/quickstart.js.map +1 -0
  154. package/dist/artifact/fsm.d.ts +41 -0
  155. package/dist/artifact/fsm.js +221 -0
  156. package/dist/artifact/fsm.js.map +1 -0
  157. package/dist/artifact/fsmDefinitions.d.ts +18 -0
  158. package/dist/artifact/fsmDefinitions.js +296 -0
  159. package/dist/artifact/fsmDefinitions.js.map +1 -0
  160. package/dist/artifact/sqliteStore.d.ts +61 -0
  161. package/dist/artifact/sqliteStore.js +381 -0
  162. package/dist/artifact/sqliteStore.js.map +1 -0
  163. package/dist/artifact/store.d.ts +49 -0
  164. package/dist/artifact/store.js +116 -0
  165. package/dist/artifact/store.js.map +1 -0
  166. package/dist/artifact/types.d.ts +535 -0
  167. package/dist/artifact/types.js +74 -0
  168. package/dist/artifact/types.js.map +1 -0
  169. package/dist/bootstrap/DependencyBootstrap.d.ts +112 -0
  170. package/dist/bootstrap/DependencyBootstrap.js +1046 -0
  171. package/dist/bootstrap/DependencyBootstrap.js.map +1 -0
  172. package/dist/bootstrap/DependencyBootstrapRenderer.d.ts +3 -0
  173. package/dist/bootstrap/DependencyBootstrapRenderer.js +138 -0
  174. package/dist/bootstrap/DependencyBootstrapRenderer.js.map +1 -0
  175. package/dist/bridge/PythonBridge.d.ts +80 -0
  176. package/dist/bridge/PythonBridge.js +437 -0
  177. package/dist/bridge/PythonBridge.js.map +1 -0
  178. package/dist/bridge/index.d.ts +2 -0
  179. package/dist/bridge/index.js +7 -0
  180. package/dist/bridge/index.js.map +1 -0
  181. package/dist/bridge/medicalWorkflows.d.ts +29 -0
  182. package/dist/bridge/medicalWorkflows.js +156 -0
  183. package/dist/bridge/medicalWorkflows.js.map +1 -0
  184. package/dist/bridge/types.d.ts +381 -0
  185. package/dist/bridge/types.js +113 -0
  186. package/dist/bridge/types.js.map +1 -0
  187. package/dist/cache/ScanCache.d.ts +41 -0
  188. package/dist/cache/ScanCache.js +120 -0
  189. package/dist/cache/ScanCache.js.map +1 -0
  190. package/dist/capabilities/BrowserCapability.d.ts +30 -0
  191. package/dist/capabilities/BrowserCapability.js +73 -0
  192. package/dist/capabilities/BrowserCapability.js.map +1 -0
  193. package/dist/capabilities/BrowserQACapability.d.ts +165 -0
  194. package/dist/capabilities/BrowserQACapability.js +438 -0
  195. package/dist/capabilities/BrowserQACapability.js.map +1 -0
  196. package/dist/capabilities/CapabilityRegistry.d.ts +17 -0
  197. package/dist/capabilities/CapabilityRegistry.js +65 -0
  198. package/dist/capabilities/CapabilityRegistry.js.map +1 -0
  199. package/dist/capabilities/ComputerCapability.d.ts +28 -0
  200. package/dist/capabilities/ComputerCapability.js +40 -0
  201. package/dist/capabilities/ComputerCapability.js.map +1 -0
  202. package/dist/capabilities/InstalledSkillsIntegration.d.ts +69 -0
  203. package/dist/capabilities/InstalledSkillsIntegration.js +240 -0
  204. package/dist/capabilities/InstalledSkillsIntegration.js.map +1 -0
  205. package/dist/capabilities/SearchCapability.d.ts +46 -0
  206. package/dist/capabilities/SearchCapability.js +88 -0
  207. package/dist/capabilities/SearchCapability.js.map +1 -0
  208. package/dist/capabilities/index.d.ts +6 -0
  209. package/dist/capabilities/index.js +9 -0
  210. package/dist/capabilities/index.js.map +1 -0
  211. package/dist/capabilities/types.d.ts +92 -0
  212. package/dist/capabilities/types.js +7 -0
  213. package/dist/capabilities/types.js.map +1 -0
  214. package/dist/cli/autofixCommands.d.ts +22 -0
  215. package/dist/cli/autofixCommands.js +32 -0
  216. package/dist/cli/autofixCommands.js.map +1 -0
  217. package/dist/cli/cortexCommands.d.ts +71 -0
  218. package/dist/cli/cortexCommands.js +335 -0
  219. package/dist/cli/cortexCommands.js.map +1 -0
  220. package/dist/cli/costCommands.d.ts +13 -0
  221. package/dist/cli/costCommands.js +48 -0
  222. package/dist/cli/costCommands.js.map +1 -0
  223. package/dist/cli/evolutionCommands.d.ts +112 -0
  224. package/dist/cli/evolutionCommands.js +246 -0
  225. package/dist/cli/evolutionCommands.js.map +1 -0
  226. package/dist/cli/gateStatusCommands.d.ts +1 -0
  227. package/dist/cli/gateStatusCommands.js +52 -0
  228. package/dist/cli/gateStatusCommands.js.map +1 -0
  229. package/dist/cli/liteCommands.d.ts +81 -0
  230. package/dist/cli/liteCommands.js +148 -0
  231. package/dist/cli/liteCommands.js.map +1 -0
  232. package/dist/cli/orchCommands.d.ts +43 -0
  233. package/dist/cli/orchCommands.js +135 -0
  234. package/dist/cli/orchCommands.js.map +1 -0
  235. package/dist/cli/phaseCommands.d.ts +248 -0
  236. package/dist/cli/phaseCommands.js +1878 -0
  237. package/dist/cli/phaseCommands.js.map +1 -0
  238. package/dist/cli/promptCommands.d.ts +1 -0
  239. package/dist/cli/promptCommands.js +57 -0
  240. package/dist/cli/promptCommands.js.map +1 -0
  241. package/dist/cli/qaCommands.d.ts +22 -0
  242. package/dist/cli/qaCommands.js +84 -0
  243. package/dist/cli/qaCommands.js.map +1 -0
  244. package/dist/cli/quickstartCommands.d.ts +17 -0
  245. package/dist/cli/quickstartCommands.js +47 -0
  246. package/dist/cli/quickstartCommands.js.map +1 -0
  247. package/dist/cli/runCommand.d.ts +39 -0
  248. package/dist/cli/runCommand.js +113 -0
  249. package/dist/cli/runCommand.js.map +1 -0
  250. package/dist/cli/scoreCommands.d.ts +1 -0
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  253. package/dist/cli/shieldCommands.d.ts +30 -0
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  256. package/dist/cli/targetCommands.d.ts +552 -0
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  259. package/dist/cli/tuiCommands.d.ts +7 -0
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  262. package/dist/cli/vibeCommands.d.ts +64 -0
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  265. package/dist/codegraph/CodeIntelligence.d.ts +147 -0
  266. package/dist/codegraph/CodeIntelligence.js +681 -0
  267. package/dist/codegraph/CodeIntelligence.js.map +1 -0
  268. package/dist/config/profiles.d.ts +64 -0
  269. package/dist/config/profiles.js +223 -0
  270. package/dist/config/profiles.js.map +1 -0
  271. package/dist/context/AntiPatternRegistry.d.ts +38 -0
  272. package/dist/context/AntiPatternRegistry.js +203 -0
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  274. package/dist/context/CavemanCompressor.d.ts +20 -0
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  277. package/dist/context/ContextBudget.d.ts +128 -0
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  280. package/dist/context/ContextBuilder.d.ts +71 -0
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  286. package/dist/context/ProjectAnatomy.d.ts +18 -0
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  289. package/dist/context/SessionStartSequence.d.ts +54 -0
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  292. package/dist/core/ExternalCommand.d.ts +9 -0
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  295. package/dist/core/GbrainRuntime.d.ts +25 -0
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  298. package/dist/core/container.d.ts +14 -0
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  307. package/dist/cortex/GovernanceMetrics.d.ts +66 -0
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  310. package/dist/cortex/InstinctExtractor.d.ts +61 -0
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  319. package/dist/cortex/SessionInjector.d.ts +44 -0
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  322. package/dist/cortex/adapters/ClaudeAdapter.d.ts +17 -0
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  325. package/dist/cortex/adapters/CodexAdapter.d.ts +10 -0
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  328. package/dist/cortex/adapters/CursorAdapter.d.ts +10 -0
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  337. package/dist/dashboard/MedicalWorkflowData.d.ts +155 -0
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  343. package/dist/dashboard/index.d.ts +4 -0
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  346. package/dist/dashboard/server.d.ts +52 -0
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  349. package/dist/env/EnvironmentDoctor.d.ts +66 -0
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package/target-research-platform/data/immune_infiltration/LUAD.csv ADDED
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package/target-research-platform/data/immune_infiltration/LUSC.csv ADDED
@@ -0,0 +1,201 @@
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30
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31
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32
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33
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34
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35
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36
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37
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38
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39
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40
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41
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42
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43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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54
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55
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56
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57
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58
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59
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60
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61
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62
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63
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64
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65
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66
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68
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69
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70
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71
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72
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73
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74
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75
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76
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77
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78
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79
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80
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81
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82
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83
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84
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85
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86
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87
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88
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89
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90
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91
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92
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94
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95
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96
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98
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99
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100
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101
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102
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103
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104
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105
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108
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109
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111
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115
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116
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117
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119
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125
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129
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130
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131
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133
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134
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135
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136
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137
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138
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139
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140
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142
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145
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150
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152
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package/target-research-platform/data/immune_infiltration/MESO.csv ADDED
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