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  1. Biouml.plugins.agentmodeling (plugin)
  2. Biouml.plugins.dropbox (plugin)
  3. Biouml.plugins.genenet (plugin)
  4. Biouml.plugins.geneways (plugin)
  5. Biouml.plugins.glycan (plugin)
  6. Biouml.plugins.gne (plugin)
  7. Biouml.plugins.googledrive (plugin)
  8. Biouml.plugins.graphml (plugin)
  9. Biouml.plugins.gxl (plugin)
  10. Biouml.plugins.matlab (plugin)
  11. Biouml.plugins.miriam (plugin)
  12. Biouml.plugins.obo (plugin)
  13. Biouml.plugins.pathfinder (plugin)
  14. Biouml.plugins.proteinmodel (plugin)
  15. Biouml.plugins.psimi (plugin)
  16. Biouml.plugins.reactome.biohub (plugin)
  17. Biouml.plugins.sabiork (plugin)
  18. Biouml.plugins.server (plugin)
  19. Biouml.plugins.simulation-test (plugin)
  20. Biouml.plugins.softberry (plugin)
  21. Biouml.plugins.stochastic (plugin)
  22. Biouml.plugins.svg (plugin)
  23. Biouml.plugins.test (plugin)
  24. Biouml.plugins.uniprot (plugin)
  25. Biouml.plugins.users (plugin)
  26. Biouml.workbench.graph (plugin)
  27. Bioumlsim
  28. C-tau
  29. COVID-19 parameters for Intestine
  30. COVID-19 parameters for Lung
  31. COVID-19 parameters for Nasopharynx
  32. CWL
  33. Calculate CMA regulation (analysis)
  34. Calculate weighted mutation score (analysis)
  35. Cell type specific TFBS prediction
  36. ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R)) (workflow)
  37. ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R)) (workflow)
  38. ChIP-Seq - Identify and classify target genes (HumanPSD(TM)) (workflow)
  39. ChIP-Seq - Identify and classify target genes (TRANSPATH(R)) (workflow)
  40. ChIP-Seq - Identify and classify target genes (workflow)
  41. ChIP-Seq - Identify composite modules on peaks (TRANSFAC(R)) (workflow)
  42. ChIP-seq Analysis
  43. Check Workflow consistency (analysis)
  44. ChromatinInfo table creation (analysis)
  45. Cistrom construction (analysis)
  46. Com.developmentontheedge.beans (plugin)
  47. Com.developmentontheedge.server (plugin)
  48. Com.developmentontheedge.util (plugin)
  49. Compare analysis results (analysis)
  50. Compute coverage by window (analysis)
  51. Compute coverage profile (analysis)
  52. Compute differentially expressed genes (Affymetrix probes) (workflow)
  53. Compute differentially expressed genes (Agilent Tox probes) (workflow)
  54. Compute differentially expressed genes (Agilent probes) (workflow)
  55. Compute differentially expressed genes (Illumina probes) (workflow)
  56. Compute differentially expressed genes using EBarrays (workflow)
  57. Compute differentially expressed genes using Hypergeometric test (Affymetrix probes) (workflow)
  58. Compute differentially expressed genes using Hypergeometric test (Agilent probes) (workflow)
  59. Compute differentially expressed genes using Hypergeometric test (Illumina probes) (workflow)
  60. Compute differentially expressed genes using Limma (workflow)
  61. Construct composite modules on tracks (without site search) (analysis)
  62. Convert identifiers for multiple gene sets (workflow)
  63. Convert table to VCF track (analysis)
  64. Convert tracks to VCF (analysis)
  65. Coverage Profiles Cutoff (analysis)
  66. Covid-19 Differential Delay Model
  67. Covid 19
  68. Covid 19 parameters
  69. Create matrix logo (analysis)
  70. Create per TF flat files (analysis)
  71. Create profile from CMA model (analysis)
  72. Create profile from matrix library (analysis)
  73. Create random track (analysis)
  74. Create tissue-specific promoter track (analysis)
  75. Create transcript region track (analysis)
  76. Cross-species identification of enriched motifs in promoters, using orthologue information (TRANSFAC(R)) (workflow)
  77. Cross-species mapping to ontologies, using orthologue information (HumanPSD(TM)) (workflow)
  78. DNase-seq Group and Profile Generation (Previous version) (analysis)
  79. DNase-seq Group and Profile Generation (analysis)
  80. Developed models
  81. Docker meta
  82. EBarrays (analysis)
  83. Enriched upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  84. Explain my genes (workflow)
  85. Export master track (analysis)
  86. Export metadata json (analysis)
  87. Export per cell clusters (analysis)
  88. Expression mapping
  89. Fast table filter (analysis)
  90. Fastq compressed (file format)
  91. Fastq mcf
  92. Fastx clip
  93. Filtering experiments by cell types (analysis)
  94. Find 10 master regulators in networks (TRANSPATH(R)) (workflow)
  95. Find 3 master regulators in networks with context genes (TRANSPATH(R)) (workflow)
  96. Find common effectors for multiple gene sets (GeneWays) (workflow)
  97. Find common effectors for multiple gene sets (TRANSPATH(R)) (workflow)
  98. Find common effectors in networks (GeneWays) (workflow)
  99. Find common effectors in networks (TRANSPATH(R)) (workflow)
  100. Find enriched TF binding sites in variation sites (TRANSFAC(R)) (workflow)
  101. Find gene fusions from RNA-seq (workflow)
  102. Find genome variants and indels from RNA-seq (workflow)
  103. Find genome variants and indels from full-genome NGS (workflow)
  104. Find master regulators for multiple gene sets (GeneWays) (workflow)
  105. Find master regulators for multiple gene sets (TRANSPATH(R)) (workflow)
  106. Find master regulators in mutated network (TRANSPATH(R)) (workflow)
  107. Find master regulators in mutated network (workflow)
  108. Find master regulators in networks (GeneWays) (workflow)
  109. Find master regulators in networks (TRANSPATH(R)) (workflow)
  110. Find master regulators in networks with context genes (TRANSPATH(R)) (workflow)
  111. Find regulatory regions with mutations (analysis)
  112. Find target genes (analysis)
  113. Flux Balance Analysis (workflow)
  114. Focused upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  115. GTEX Mutation effect on sites (analysis)
  116. GTRD comparison
  117. GTRD statistics
  118. GWAS format
  119. Galaxy
  120. Galaxy admin
  121. Galaxy cloud
  122. Gene expression prediction
  123. Gene set enrichment analysis (Affymetrix probes) (workflow)
  124. Gene set enrichment analysis (Agilent probes) (workflow)
  125. Gene set enrichment analysis (Gene table) (workflow)
  126. Gene set enrichment analysis (Illumina probes) (workflow)
  127. Gene set enrichment analysis - select a classification (Gene table) (workflow)
  128. Gene set enrichment analysis HumanPSD (Affymetrix probes) (workflow)
  129. Gene set enrichment analysis HumanPSD (Agilent probes) (workflow)
  130. Gene set enrichment analysis HumanPSD (Gene table) (workflow)
  131. Gene set enrichment analysis HumanPSD (Illumina probes) (workflow)
  132. Generate Table From JSON (analysis)
  133. Get miRNA targets (analysis)
  134. GlycanR (analysis)
  135. Guided linear model analysis
  136. Hadoop
  137. Hash parameters
  138. Headless BioUML
  139. Heatmap (analysis)
  140. Hypergeometric analysis for multiple inputs (workflow)
  141. IPython format
  142. Identify composite modules in promoters (TRANSFAC(R)) (workflow)
  143. Identify enriched composite modules in promoters (GTRD) (workflow)
  144. Identify enriched composite modules in promoters (TRANSFAC(R)) (workflow)
  145. Identify enriched motifs in promoters (GTRD) (workflow)
  146. Identify enriched motifs in promoters (TRANSFAC(R)) (workflow)
  147. Identify enriched motifs in tissue specific promoters (TRANSFAC(R)) (workflow)
  148. Identify enriched motifs in tissue specific tracks (TRANSFAC(R)) (workflow)
  149. Identify enriched motifs in tracks (TRANSFAC(R)) (workflow)
  150. Illumina microarray file
  151. Import from BC Platform (analysis)
  152. Import from TranSMART (analysis)
  153. Install HumanPSD(TM) database (analysis)
  154. Intersect tables (analysis)
  155. Intersect tracks (analysis)
  156. Join two tables (analysis)
  157. Jupyter
  158. Kinetic parameters for COVID-19 models
  159. LRPath (analysis)
  160. Landing
  161. Limma (analysis)
  162. MEALR (tracks) (analysis)
  163. MSAT (analysis)
  164. Mapping to GO ontologies and comparison for two gene sets (workflow)
  165. Mapping to ontologies (Gene table) (workflow)
  166. Mapping to ontologies (HumanPSD(TM)) (workflow)
  167. Mapping to ontologies (TRANSPATH(R)) (workflow)
  168. Mapping to ontologies and comparison for two gene sets (HumanPSD(TM)) (workflow)
  169. Mapping to ontologies and comparison for two gene sets (TRANSPATH(R)) (workflow)
  170. Mapping to ontologies for multiple gene sets (HumanPSD(TM)) (workflow)
  171. Mapping to ontologies for multiple gene sets (TRANSPATH(R)) (workflow)
  172. Mapping to ontologies for multiple gene sets (workflow)
  173. Mapping to ontology - select a classification (2 Gene tables) (workflow)
  174. Mapping to ontology - select a classification (Gene table) (workflow)
  175. Mapping to ontology - select a classification (Multiple Gene tables) (workflow)
  176. MiRNA feed forward loops (analysis)
  177. Model analysis
  178. Modeling Antihypertensive drugs
  179. Modeling cardiovascular system
  180. Muscle metabolism
  181. Mutation effect on sites advanced (analysis)
  182. N-Glycan biosynthesis
  183. NGS misc
  184. Non-Linear Mixed Effects Model
  185. Normalization quality plots (analysis)
  186. Normalize Affymetrix experiment and control (analysis)
  187. Normalize Agilent experiment and control (analysis)
  188. Normalize Illumina experiment and control (analysis)
  189. Open regulated genes table (analysis)
  190. Outer join (analysis)
  191. PCA (analysis)
  192. Patient-specific cardiovascular model
  193. Peaks to matrices (workflow)
  194. Population generation (analysis)
  195. Prediction of miRNA binding sites (workflow)
  196. Prepare target genes by expression (analysis)
  197. Product
  198. Profiles Statistics (analysis)
  199. QUAST
  200. Quantification of RNA-seq in BAM format for mouse mm9 single end (workflow)
  201. Quantification of RNA-seq in FASTQ format for mouse mm9 single end (workflow)
  202. Quantification of RNA-seq with Cufflinks (no de-novo assembly) for FASTQ files (workflow)
  203. Quantification of RNA-seq with Cufflinks (with de-novo assembly) for FASTQ files (workflow)
  204. Quantification of RNA-seq with Cufflinks for multiple BAM files (workflow)
  205. RAGOUT
  206. RNA-Seq analysis
  207. Reads to matrices (workflow)
  208. Reduce track (analysis)
  209. Remote application client (analysis)
  210. Ru.biosoft.access.search (plugin)
  211. Ru.biosoft.bsa.server (plugin)
  212. Ru.biosoft.exception (plugin)
  213. Ru.biosoft.fs (plugin)
  214. Ru.biosoft.graphics (plugin)
  215. Ru.biosoft.jobcontrol (plugin)
  216. Ru.biosoft.math (plugin)
  217. Ru.biosoft.plugins.graph (plugin)
  218. Ru.biosoft.server.tomcat (plugin)
  219. Ru.biosoft.services (plugin)
  220. Ru.biosoft.treetable (plugin)
  221. Ru.biosoft.vm (plugin)
  222. Ru.biosoft.works (plugin)
  223. Run analysis
  224. SBGN extension
  225. SPAdes
  226. SRA to FASTQ (workflow)
  227. Search for enriched TFBSs (genes) (analysis)
  228. Search for enriched TFBSs (tracks) (analysis)
  229. Search for self-regulating transcription factors (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  230. Search regulated genes (analysis)
  231. Select files from folder (analysis)
  232. Server ICT
  233. Servers
  234. Site Profile Filtering (analysis)
  235. Site Size Filtering (analysis)
  236. Site prediction
  237. Sites Motifs Analysis
  238. Sites Open Chromatin Statistics (analysis)
  239. Sites Open Chromatin Statistics For Folders (analysis)
  240. Sites genome location (analysis)
  241. Sites genome location for folders (analysis)
  242. Steady State Examples
  243. Stub process file (analysis)
  244. Systems biology - model import 02
  245. TF binding sites prediction in genome or track (analysis)
  246. Tools Comparison 2022
  247. TrackInfo table creation (analysis)
  248. Tutorials
  249. Update master track (analysis)
  250. Upstream analysis (TRANSFAC(R) and GeneWays) (workflow)

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