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

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