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  1. 1-dimensional arterial tree model
  2. 3D viewer
  3. AUC Estimation For meta-cluster track (analysis)
  4. About dialog (extension point)
  5. Acknowledgements
  6. Adaptive simulated annealing (analysis)
  7. Add calculated column (analysis)
  8. Add expression values (analysis)
  9. Add genes from CMA (analysis)
  10. Add reactants (analysis)
  11. Affymetrix CEL file
  12. Affymetrix normalization (analysis)
  13. Agilent microarray file
  14. Agilent normalization (analysis)
  15. Algebraic steady state (analysis)
  16. Analyses (extension point)
  17. Analysis (element type)
  18. Analysis method development
  19. Analysis of Binding Regions (analysis)
  20. Analysis of Cis-Regulatory Modules (analysis)
  21. Analyze SNP list (GTRD) (workflow)
  22. Analyze SNP list (TRANSFAC(R)) (workflow)
  23. Analyze any DNA sequence, EMBL (workflow)
  24. Analyze any DNA sequence, Fasta (workflow)
  25. Analyze any DNA sequence, GeneBank (workflow)
  26. Analyze any DNA sequence (GTRD) (workflow)
  27. Analyze any DNA sequence (TRANSFAC(R)) (workflow)
  28. Analyze any DNA sequence for site enrichment (GTRD) (workflow)
  29. Analyze any DNA sequence for site enrichment (TRANSFAC(R)) (workflow)
  30. Analyze miRNA target enrichment (analysis)
  31. Analyze promoters (GTRD) (workflow)
  32. Analyze promoters (TRANSFAC(R)) (workflow)
  33. Annotate diagram (analysis)
  34. Annotate table (analysis)
  35. Annotate track with genes (analysis)
  36. Annotation (extension point)
  37. Antimony
  38. Antimony (file format)
  39. Application log (viewpart)
  40. Apply CMA model to tracks (analysis)
  41. Apply events (analysis)
  42. Apply state to diagram (analysis)
  43. ArticleComparator (analysis)
  44. ArticleTrackCreator (analysis)
  45. Autosome.Ru
  46. BAM filter multi-hits (analysis)
  47. BAM filter strand specific (analysis)
  48. BED format
  49. BPMN
  50. Beans (extension point)
  51. Binding regions summary (analysis)
  52. BioBlend
  53. BioCloudCentral
  54. BioGears
  55. BioHub
  56. BioNetGen
  57. BioNetGen language format
  58. BioPAX file
  59. BioStore
  60. BioUML
  61. BioUML - systems biology
  62. BioUML Development Kit
  63. BioUML Simulation result (file format)
  64. BioUML development history
  65. BioUML development roadmap
  66. BioUML exceptions
  67. BioUML format
  68. BioUML installation
  69. BioUML overview
  70. BioUML server
  71. BioUML server installation
  72. BioUML team
  73. BioUML user interface
  74. BioUML web client
  75. BioUML web edition
  76. BioUML wiki
  77. BioUML workbench
  78. BioUML workbench installation
  79. Biohub (extension point)
  80. Biohub (host object)
  81. Biomodels
  82. Biopath
  83. Biouml.plugins.affymetrix (plugin)
  84. Biouml.plugins.agentmodeling (plugin)
  85. Biouml.plugins.agilent (plugin)
  86. Biouml.plugins.antimony (plugin)
  87. Biouml.plugins.bindingregions (plugin)
  88. Biouml.plugins.bionetgen (plugin)
  89. Biouml.plugins.biopax (plugin)
  90. Biouml.plugins.bkl (plugin)
  91. Biouml.plugins.bowtie (plugin)
  92. Biouml.plugins.ccsignature (plugin)
  93. Biouml.plugins.cellml (plugin)
  94. Biouml.plugins.chebi (plugin)
  95. Biouml.plugins.chemoinformatics (plugin)
  96. Biouml.plugins.chipmunk (plugin)
  97. Biouml.plugins.cma (plugin)
  98. Biouml.plugins.creasemarks (plugin)
  99. Biouml.plugins.cytoscape (plugin)
  100. Biouml.plugins.das (plugin)
  101. Biouml.plugins.download (plugin)
  102. Biouml.plugins.dropbox (plugin)
  103. Biouml.plugins.endonet (plugin)
  104. Biouml.plugins.enrichment (plugin)
  105. Biouml.plugins.ensembl (plugin)
  106. Biouml.plugins.expasy (plugin)
  107. Biouml.plugins.expression (plugin)
  108. Biouml.plugins.fbc (plugin)
  109. Biouml.plugins.genemodels (plugin)
  110. Biouml.plugins.genenet (plugin)
  111. Biouml.plugins.geneways (plugin)
  112. Biouml.plugins.genomeenhancer (plugin)
  113. Biouml.plugins.ginsim (plugin)
  114. Biouml.plugins.glycan (plugin)
  115. Biouml.plugins.gne (plugin)
  116. Biouml.plugins.go (plugin)
  117. Biouml.plugins.googledrive (plugin)
  118. Biouml.plugins.graphml (plugin)
  119. Biouml.plugins.gtrd (plugin)
  120. Biouml.plugins.gxl (plugin)
  121. Biouml.plugins.hemodynamics (plugin)
  122. Biouml.plugins.illumina (plugin)
  123. Biouml.plugins.kegg (plugin)
  124. Biouml.plugins.keynodes (plugin)
  125. Biouml.plugins.lucene (plugin)
  126. Biouml.plugins.machinelearning (plugin)
  127. Biouml.plugins.matlab (plugin)
  128. Biouml.plugins.metabolics (plugin)
  129. Biouml.plugins.microarray (plugin)
  130. Biouml.plugins.mirbase (plugin)
  131. Biouml.plugins.miriam (plugin)
  132. Biouml.plugins.mirprom (plugin)
  133. Biouml.plugins.modelreduction (plugin)
  134. Biouml.plugins.node (plugin)
  135. Biouml.plugins.obo (plugin)
  136. Biouml.plugins.optimization (plugin)
  137. Biouml.plugins.pass (plugin)
  138. Biouml.plugins.pathfinder (plugin)
  139. Biouml.plugins.perfectosape (plugin)
  140. Biouml.plugins.pharm (plugin)
  141. Biouml.plugins.proteinmodel (plugin)
  142. Biouml.plugins.psimi (plugin)
  143. Biouml.plugins.reactome.biohub (plugin)
  144. Biouml.plugins.reactome (plugin)
  145. Biouml.plugins.research (plugin)
  146. Biouml.plugins.riboseqArticleResult (plugin)
  147. Biouml.plugins.riboseq (plugin)
  148. Biouml.plugins.sabiork (plugin)
  149. Biouml.plugins.sbgn (plugin)
  150. Biouml.plugins.sbml (plugin)
  151. Biouml.plugins.sbw (plugin)
  152. Biouml.plugins.sedml (plugin)
  153. Biouml.plugins.seek (plugin)
  154. Biouml.plugins.server (plugin)
  155. Biouml.plugins.simulation-test (plugin)
  156. Biouml.plugins.simulation (plugin)
  157. Biouml.plugins.softberry (plugin)
  158. Biouml.plugins.stochastic (plugin)
  159. Biouml.plugins.svg (plugin)
  160. Biouml.plugins.test (plugin)
  161. Biouml.plugins.transfac (plugin)
  162. Biouml.plugins.transpath (plugin)
  163. Biouml.plugins.uniprot (plugin)
  164. Biouml.plugins.users (plugin)
  165. Biouml.plugins.wiki (plugin)
  166. Biouml.workbench.graph (plugin)
  167. Biouml.workbench (plugin)
  168. Bioumlsim
  169. Blast alignment coverage (analysis)
  170. Bowtie (analysis)
  171. Breakdancer output (file format)
  172. Bsa (host object)
  173. BuildASiteOffsetTable (analysis)
  174. BuildProfileModel (analysis)
  175. Building Flux Balance DataTable (analysis)
  176. C-tau
  177. CMA Result Statistic (analysis)
  178. CNVnator genotype output (file format)
  179. COVID-19 parameters for Intestine
  180. COVID-19 parameters for Lung
  181. COVID-19 parameters for Nasopharynx
  182. CRC Analysis
  183. CRISPR Cas9 and specific oligonucleotides (analysis)
  184. CR cluster selector (analysis)
  185. CWL
  186. Calculate CMA regulation (analysis)
  187. Calculate TFs regulatory score (analysis)
  188. Calculate keynodes ranks (analysis)
  189. Calculate weighted mutation score (analysis)
  190. Categories (reference type)
  191. Categories - BKL
  192. Categories - ExPASy
  193. Categories - GTRD
  194. Categories - Gene ontology
  195. Cdk (host object)
  196. CellML (file format)
  197. Cell - EndoNet
  198. Cell type specific TFBS prediction
  199. Cellular genetic algorithm (analysis)
  200. ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R)) (workflow)
  201. ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R)) (workflow)
  202. ChIP-Seq - Identify and classify target genes (HumanPSD(TM)) (workflow)
  203. ChIP-Seq - Identify and classify target genes (TRANSPATH(R)) (workflow)
  204. ChIP-Seq - Identify and classify target genes (workflow)
  205. ChIP-Seq - Identify composite modules on peaks (TRANSFAC(R)) (workflow)
  206. ChIP-Seq characteristics distribution (analysis)
  207. ChIP-Seq peaks clusterization (analysis)
  208. ChIP-seq Analysis
  209. ChIP-seq Quality control analysis
  210. ChIP-seq peak profile (analysis)
  211. ChIP-seq peaks - GTRD
  212. ChIPHorde (analysis)
  213. ChIPMunk (analysis)
  214. ChIPMunk (perspective)
  215. ChIP experiment - GTRD
  216. Change diagram (analysis)
  217. Change profile cutoffs (analysis)
  218. Check Workflow consistency (analysis)
  219. Check quotas (analysis)
  220. Chipmunk (host object)
  221. ChromatinInfo table creation (analysis)
  222. Chromosome enrichment (analysis)
  223. Cis-module identification (analysis)
  224. Cis-module sets near given genes (analysis)
  225. Cistrom construction (analysis)
  226. Classification analysis
  227. Classification analysis advanced (analysis)
  228. Classification hub
  229. Clean up SQL database (analysis)
  230. CloudBioLinux
  231. CloudMan
  232. Cluster analysis
  233. Cluster analysis by K-means (analysis)
  234. Cluster by path (analysis)
  235. Cluster by shortest path (analysis)
  236. Cluster track (analysis)
  237. Collaborative diagram editing
  238. Colon cancer signature2 (analysis)
  239. Colon cancer signature (analysis)
  240. Color space to nucleotide (analysis)
  241. Com.developmentontheedge.beans (plugin)
  242. Com.developmentontheedge.server (plugin)
  243. Com.developmentontheedge.util (plugin)
  244. Combined track
  245. Common and IPS scores correlation (analysis)
  246. Common class (extension point)
  247. Compare Experiments (analysis)
  248. Compare TFBS mutations (analysis)
  249. Compare analysis results (analysis)
  250. Compare site models (analysis)
  251. Composite module to proteins (analysis)
  252. ComputeProfileSums (analysis)
  253. ComputeTranscriptProfile (analysis)
  254. Compute coverage by window (analysis)
  255. Compute coverage profile (analysis)
  256. Compute differentially expressed genes (Affymetrix probes) (workflow)
  257. Compute differentially expressed genes (Agilent Tox probes) (workflow)
  258. Compute differentially expressed genes (Agilent probes) (workflow)
  259. Compute differentially expressed genes (Illumina probes) (workflow)
  260. Compute differentially expressed genes using EBarrays (workflow)
  261. Compute differentially expressed genes using Hypergeometric test (Affymetrix probes) (workflow)
  262. Compute differentially expressed genes using Hypergeometric test (Agilent probes) (workflow)
  263. Compute differentially expressed genes using Hypergeometric test (Illumina probes) (workflow)
  264. Compute differentially expressed genes using Limma (workflow)
  265. Compute profile thresholds (analysis)
  266. Construct IPS CisModule (analysis)
  267. Construct composite modules (analysis)
  268. Construct composite modules on track (correlation) (analysis)
  269. Construct composite modules on tracks (analysis)
  270. Construct composite modules on tracks (without site search) (analysis)
  271. Construct composite modules on tracks with keynodes (analysis)
  272. Construct composite modules with keynodes (analysis)
  273. Context item (extension point)
  274. Continue CMA (analysis)
  275. Contributors
  276. Convert diagram to Transpath (analysis)
  277. Convert diagram to pairs (analysis)
  278. Convert files to tracks (analysis)
  279. Convert genomic BAM to transcriptomic (analysis)
  280. Convert identifiers for multiple gene sets (workflow)
  281. Convert site models to proteins (analysis)
  282. Convert site search summary (analysis)
  283. Convert table (analysis)
  284. Convert table to VCF track (analysis)
  285. Convert table to track (analysis)
  286. Convert table via homology (analysis)
  287. Convert tracks to VCF (analysis)
  288. Copy data element (analysis)
  289. Copy folder (analysis)
  290. Correlation Analysis
  291. Correlations of best sites (analysis)
  292. Count olig frequencies (analysis)
  293. Count reads in transcripts (analysis)
  294. CoverageCheker (analysis)
  295. Coverage Profiles Cutoff (analysis)
  296. Covid-19 Differential Delay Model
  297. Covid 19
  298. Covid 19 parameters
  299. Creasemarks analysis
  300. Create DAS track (analysis)
  301. Create IPS model (analysis)
  302. Create Match model (analysis)
  303. Create custom project (analysis)
  304. Create database from diagram (analysis)
  305. Create flat files (analysis)
  306. Create folder (analysis)
  307. Create matrix by mixture of normal components (analysis)
  308. Create matrix logo (analysis)
  309. Create miRNA promoters (analysis)
  310. Create per TF flat files (analysis)
  311. Create profile from CMA model (analysis)
  312. Create profile from gene table (analysis)
  313. Create profile from matrix library (analysis)
  314. Create profile from site model table (analysis)
  315. Create random track (analysis)
  316. Create state (analysis)
  317. Create tissue-specific promoter track (analysis)
  318. Create transcript region track (analysis)
  319. Create weight matrix model (analysis)
  320. Creating Galaxy tool
  321. Cross-species identification of enriched motifs in promoters, using orthologue information (TRANSFAC(R)) (workflow)
  322. Cross-species mapping to ontologies, using orthologue information (HumanPSD(TM)) (workflow)
  323. Cross cost grid layout
  324. Cytoscape network format
  325. DAE Models examples
  326. DDMoRe consortium
  327. DNase-seq Group and Profile Generation (Previous version) (analysis)
  328. DNase-seq Group and Profile Generation (analysis)
  329. Danon et al. Covid-19 transmission in England
  330. Das (host object)
  331. DataFilter (host object)
  332. Data (host object)
  333. Data collection listener (extension point)
  334. Data matrix operations (analysis)
  335. Databases
  336. Databases installation
  337. Default (perspective)
  338. Defines.js
  339. Descrete events
  340. Developed models
  341. DiChIPHorde (analysis)
  342. DiChIPMunk (analysis)
  343. Diagram (element type)
  344. Diagram document
  345. Diagram editing history
  346. Diagram graph compare analysis
  347. Diagram to user hub collection (analysis)
  348. Diagram type
  349. Diagram view part (extension point)
  350. Diff manager (extension point)
  351. Differential expression with DESeq (analysis)
  352. Disease - MeSH
  353. Distinct TF classes (analysis)
  354. Docker meta
  355. Document factory (extension point)
  356. Document pane
  357. Dormand-Prince
  358. Double encode SOLiD (analysis)
  359. Download
  360. Download model (analysis)
  361. Drugs - DrugBank
  362. EBarrays (analysis)
  363. EMBL format
  364. Effector search (analysis)
  365. Element action (extension point)
  366. Element type
  367. Encode quality metrics estimation (analysis)
  368. Enhance Score (analysis)
  369. Enriched upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  370. Enrichment (host object)
  371. Enrichment analysis
  372. Ensembl
  373. Ensembl (host object)
  374. Ensembl installation
  375. Enzymes - ExPASy
  376. Enzymes - KEGG
  377. Estimate read density (analysis)
  378. Euler
  379. Evolution strategy (SRES) (analysis)
  380. Explain my genes (workflow)
  381. Export (extension point)
  382. Export element (analysis)
  383. Export master track (analysis)
  384. Export metadata json (analysis)
  385. Export per cell clusters (analysis)
  386. Expression mapping
  387. Extend network (analysis)
  388. Extract RNA length (analysis)
  389. Extract ribosomal RNA (analysis)
  390. Fantom analysis
  391. Fast table filter (analysis)
  392. Fasta format
  393. Fastq compressed (file format)
  394. Fastq format
  395. Fastq mcf
  396. Fastx clip
  397. Features
  398. File (element type)
  399. Filter SPAdes output
  400. Filter duplicate rows (analysis)
  401. Filter one track by another (analysis)
  402. Filter table (analysis)
  403. Filter track by condition (analysis)
  404. Filtering experiments by cell types (analysis)
  405. Filtration of predicted sites by filters (analysis)
  406. Find 10 master regulators in networks (TRANSPATH(R)) (workflow)
  407. Find 3 master regulators in networks with context genes (TRANSPATH(R)) (workflow)
  408. Find common effectors for multiple gene sets (GeneWays) (workflow)
  409. Find common effectors for multiple gene sets (TRANSPATH(R)) (workflow)
  410. Find common effectors in networks (GeneWays) (workflow)
  411. Find common effectors in networks (TRANSPATH(R)) (workflow)
  412. Find enriched TF binding sites in variation sites (TRANSFAC(R)) (workflow)
  413. Find gene fusions from RNA-seq (workflow)
  414. Find genome variants and indels from RNA-seq (workflow)
  415. Find genome variants and indels from full-genome NGS (workflow)
  416. Find longest connected chains (analysis)
  417. Find master regulators for multiple gene sets (GeneWays) (workflow)
  418. Find master regulators for multiple gene sets (TRANSPATH(R)) (workflow)
  419. Find master regulators in mutated network (TRANSPATH(R)) (workflow)
  420. Find master regulators in mutated network (workflow)
  421. Find master regulators in networks (GeneWays) (workflow)
  422. Find master regulators in networks (TRANSPATH(R)) (workflow)
  423. Find master regulators in networks with context genes (TRANSPATH(R)) (workflow)
  424. Find miRNA feed forward loops with CMA (analysis)
  425. Find regulatory regions (analysis)
  426. Find regulatory regions with mutations (analysis)
  427. Find shortest path between two sets (analysis)
  428. Find target genes (analysis)
  429. Find unmappable regions (analysis)
  430. FinderArticlePoints (analysis)
  431. Flux Balance Analysis (workflow)
  432. Flux Balance Constraint (analysis)
  433. Flux balance analysis
  434. Focused upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  435. Fold-Change calculation (analysis)
  436. Folder (element type)
  437. Force directed layout
  438. Ftp (host object)
  439. Function (extension point)
  440. Functional classification (analysis)
  441. Functional classification by diagrams (analysis)
  442. GC island finder (analysis)
  443. GLBSOLVE (analysis)
  444. GO installation
  445. GTEX Mutation effect on sites (analysis)
  446. GTRD
  447. GTRD (perspective)
  448. GTRD Workflow
  449. GTRD analysis
  450. GTRD analysis advanced (analysis)
  451. GTRD comparison
  452. GTRD statistics
  453. GWAS format
  454. Galaxy
  455. Galaxy (host object)
  456. Galaxy admin
  457. Galaxy cloud
  458. Galaxy installation
  459. Galaxy method (element type)
  460. Gathering genome statistics (analysis)
  461. GenBank format
  462. GeneNet
  463. GeneXplain
  464. GeneXplain GmbH
  465. Gene Ontology
  466. Gene Transfer Format
  467. Gene expression prediction
  468. Gene features (analysis)
  469. Gene overlap statistics (analysis)
  470. Gene set enrichment analysis (Affymetrix probes) (workflow)
  471. Gene set enrichment analysis (Agilent probes) (workflow)
  472. Gene set enrichment analysis (Gene table) (workflow)
  473. Gene set enrichment analysis (Illumina probes) (workflow)
  474. Gene set enrichment analysis - select a classification (Gene table) (workflow)
  475. Gene set enrichment analysis HumanPSD (Affymetrix probes) (workflow)
  476. Gene set enrichment analysis HumanPSD (Agilent probes) (workflow)
  477. Gene set enrichment analysis HumanPSD (Gene table) (workflow)
  478. Gene set enrichment analysis HumanPSD (Illumina probes) (workflow)
  479. Gene set to track (analysis)
  480. General Feature Format
  481. General control panel
  482. Generate Table From JSON (analysis)
  483. Generate dynamic model (analysis)
  484. Generate workflow from annotation diagram (analysis)
  485. Generic file
  486. Genes (reference type)
  487. Genes - BKL
  488. Genes - Ensembl
  489. Genes - Entrez
  490. Genes - GenBank
  491. Genes - Gene symbol
  492. Genes - Illumina
  493. Genes - Transpath
  494. Genes - Unigene
  495. Geneways
  496. Genome Browser iframe
  497. Genome Browser json
  498. Genome browser
  499. Genome coverage (analysis)
  500. Get miRNA targets (analysis)

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