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  1. Get transcripts track (analysis)
  2. GinSim (file format)
  3. GlycanR (analysis)
  4. Glycan structures
  5. Graph search
  6. Grid layout
  7. Group table rows (analysis)
  8. Guided linear model analysis
  9. HTML file
  10. Hadoop
  11. Hash parameters
  12. Headless BioUML
  13. Heatmap (analysis)
  14. Hemodynamics model (file format)
  15. Heterozygous site caller (analysis)
  16. Hierarchical layout
  17. Hormone - EndoNet
  18. Host object (extension point)
  19. Html (element type)
  20. HumanSim
  21. Hypergeometric analysis
  22. Hypergeometric analysis for multiple inputs (workflow)
  23. IPS-scores in SNPs (analysis)
  24. IPS ROC-curves (analysis)
  25. IPS motif discovery (analysis)
  26. IPS prediction (analysis)
  27. IPython format
  28. Identical best site ROC-curves (analysis)
  29. Identification of cis-regulatory modules with given pattern of TF-classes (analysis)
  30. Identification of composite elements by filters (analysis)
  31. Identify composite modules in promoters (TRANSFAC(R)) (workflow)
  32. Identify enriched composite modules in promoters (GTRD) (workflow)
  33. Identify enriched composite modules in promoters (TRANSFAC(R)) (workflow)
  34. Identify enriched motifs in promoters (GTRD) (workflow)
  35. Identify enriched motifs in promoters (TRANSFAC(R)) (workflow)
  36. Identify enriched motifs in tissue specific promoters (TRANSFAC(R)) (workflow)
  37. Identify enriched motifs in tissue specific tracks (TRANSFAC(R)) (workflow)
  38. Identify enriched motifs in tracks (TRANSFAC(R)) (workflow)
  39. Illumina metylation probes to track (analysis)
  40. Illumina microarray file
  41. Illumina normalization (analysis)
  42. Image (element type)
  43. Image file
  44. Import (extension point)
  45. Import HOCOMOCO (analysis)
  46. Import ensembl homology (analysis)
  47. Import from BC Platform (analysis)
  48. Import from TranSMART (analysis)
  49. Infer network (analysis)
  50. Information box
  51. Install ExPASy (analysis)
  52. Install HumanPSD(TM) database (analysis)
  53. Install Reactome (analysis)
  54. Install TRANSFAC(R) database (analysis)
  55. Install TRANSPATH(R) database (analysis)
  56. Institute of Systems Biology
  57. Intersect tables (analysis)
  58. Intersect tracks (analysis)
  59. Interval format
  60. Isoform TE (analysis)
  61. Isoforms - GTRD
  62. JVODE
  63. Join GTRD Tracks (analysis)
  64. Join GTRD clusters (analysis)
  65. Join diagrams (analysis)
  66. Join several tables (analysis)
  67. Join table (analysis)
  68. Join tracks (analysis)
  69. Join two tables (analysis)
  70. Jupyter
  71. KEGG (reference type)
  72. KeyNodes hub
  73. Key Node Sensitivity Analysis
  74. Kinetic parameters for COVID-19 models
  75. LRPath (analysis)
  76. LS-regression analysis
  77. Landing
  78. Large sequence minimal unique length (analysis)
  79. Layout (extension point)
  80. Limma (analysis)
  81. LincRNA and mRNA features (analysis)
  82. Linear Shifted Model (analysis)
  83. Locations of best sites (analysis)
  84. Long-term model of the CVS/Renal system
  85. Look and feel (extension point)
  86. Lucene indexes creation
  87. MEALR (tracks) (analysis)
  88. MGL
  89. MSAT (analysis)
  90. Make GTF for riboseq alignment (analysis)
  91. Make meta tracks (analysis)
  92. Manual parameter fitting
  93. Map Transfac sites to genome (analysis)
  94. Map to Transpath (analysis)
  95. Mappability histogram (analysis)
  96. Mapping to GO ontologies and comparison for two gene sets (workflow)
  97. Mapping to ontologies (Gene table) (workflow)
  98. Mapping to ontologies (HumanPSD(TM)) (workflow)
  99. Mapping to ontologies (TRANSPATH(R)) (workflow)
  100. Mapping to ontologies and comparison for two gene sets (HumanPSD(TM)) (workflow)
  101. Mapping to ontologies and comparison for two gene sets (TRANSPATH(R)) (workflow)
  102. Mapping to ontologies for multiple gene sets (HumanPSD(TM)) (workflow)
  103. Mapping to ontologies for multiple gene sets (TRANSPATH(R)) (workflow)
  104. Mapping to ontologies for multiple gene sets (workflow)
  105. Mapping to ontology - select a classification (2 Gene tables) (workflow)
  106. Mapping to ontology - select a classification (Gene table) (workflow)
  107. Mapping to ontology - select a classification (Multiple Gene tables) (workflow)
  108. Mass Conservation Analysis
  109. Match genes and metabolites (analysis)
  110. Matching BioHub
  111. Matrices (reference type)
  112. Matrices - GTRD
  113. Matrices - TRANSFAC
  114. Matrix (element type)
  115. Matrix comparison (analysis)
  116. Matrix derivation (analysis)
  117. Matrix library (element type)
  118. Mature-miRNA - miRBase
  119. Merge binding regions for cell-lines (analysis)
  120. Merge peak callers (analysis)
  121. Merge peaks (analysis)
  122. Merge simulation results (analysis)
  123. Merge table columns (analysis)
  124. Merge track statistics (analysis)
  125. Meta analysis
  126. Metabolic Control Analysis
  127. Metabolic control analysis example
  128. Method (extension point)
  129. Method description HTML file
  130. Methylation probes - Illumina
  131. MiRNA - miRBase
  132. MiRNA feed forward loops (analysis)
  133. MicroRNA aligner (analysis)
  134. MicroRNA finder (analysis)
  135. Microarray (host object)
  136. Mixture of normal components (analysis)
  137. ModelReduction (host object)
  138. Model (host object)
  139. Model analysis
  140. Modeling Antihypertensive drugs
  141. Modeling cardiovascular system
  142. Modular model of the human CVS v.1
  143. Modular model of the human CVS v.2
  144. Modular modeling
  145. Module type (extension point)
  146. Motif quality analysis
  147. Moved class (extension point)
  148. Multivariate regression analysis
  149. Multivariate sample analysis
  150. Muscle metabolism
  151. Mutation effect (analysis)
  152. Mutation effect on sites (analysis)
  153. Mutation effect on sites advanced (analysis)
  154. Mutations to genes with weights (analysis)
  155. N-Glycan biosynthesis
  156. NGS misc
  157. Network (host object)
  158. New BioStore
  159. Node (host object)
  160. Non-Linear Mixed Effects Model
  161. Non-merged ChIP-Seq tracks summary (analysis)
  162. Nonlinear Model (analysis)
  163. Normalization quality plots (analysis)
  164. Normalize (host object)
  165. Normalize Affymetrix experiment and control (analysis)
  166. Normalize Agilent experiment and control (analysis)
  167. Normalize Illumina experiment and control (analysis)
  168. Oligonucleotides in sequence samples (analysis)
  169. Open per TF view (analysis)
  170. Open regulated genes table (analysis)
  171. Open tracks for all TF (analysis)
  172. Optimization (host object)
  173. Optimization document
  174. Optimization examples
  175. Optimization problem
  176. Orthogonal layout
  177. Outer join (analysis)
  178. Overall circulation model
  179. PASS analysis
  180. PCA (analysis)
  181. PSD pharmaceutical compounds analysis
  182. Parameter fitting (analysis)
  183. Parameter identifiability (optimization) (analysis)
  184. Parameter identifiability (table) (analysis)
  185. Parameter identifiability example
  186. Particle swarm optimization (analysis)
  187. Pathways (reference type)
  188. Pathways - Reactome
  189. Pathways - Transpath
  190. Patient-specific cardiovascular model
  191. Peak finders comparison (analysis)
  192. Peaks to matrices (workflow)
  193. Perfectosape (analysis)
  194. Perfectosape (host object)
  195. Perspective
  196. Perspective (extension point)
  197. PharmML
  198. Pharmaceutical Compounds analysis
  199. Pindel output (file format)
  200. Plot2D (analysis)
  201. Plot bar chart (analysis)
  202. Plot pie chart (analysis)
  203. Plot scatter chart (analysis)
  204. Plugin development
  205. Polynomial Regression analysis
  206. Population generation (analysis)
  207. PredictStartSites (analysis)
  208. Prediction of TF-binding sites of given TF (analysis)
  209. Prediction of miRNA binding sites (workflow)
  210. Prepare GTF annotation (analysis)
  211. Prepare Search by regulation (analysis)
  212. Prepare cluster to exp table (analysis)
  213. Prepare finished tables (analysis)
  214. Prepare target genes by expression (analysis)
  215. Preprocess raw reads (analysis)
  216. Preprocessor (extension point)
  217. Presentations
  218. Probes (reference type)
  219. Probes - Affymetrix
  220. Probes - Affymetrix HG-U133+ PM
  221. Probes - Affymetrix HTA-2-0
  222. Probes - Affymetrix HuGene-2-0-st
  223. Probes - Affymetrix HuGene-2-1-st
  224. Probes - Affymetrix RaGene-2-0-st
  225. Probes - Affymetrix ST
  226. Probes - Affymetrix miRNA-1-0
  227. Probes - Affymetrix miRNA-2-0
  228. Probes - Affymetrix miRNA-3-0
  229. Probes - Affymetrix miRNA-4-0
  230. Probes - Agilent
  231. Probes - Agilent Tox Array
  232. Probes - Illumina
  233. Process track with sites (analysis)
  234. Product
  235. Profile (element type)
  236. Profiles Statistics (analysis)
  237. Project
  238. Proteins (reference type)
  239. Proteins - BKL
  240. Proteins - EndoNet
  241. Proteins - Ensembl
  242. Proteins - GTRD
  243. Proteins - GenBank
  244. Proteins - IPI
  245. Proteins - NCBI
  246. Proteins - PDB
  247. Proteins - Reactome
  248. Proteins - RefSeq
  249. Proteins - Transfac
  250. Proteins - Transpath
  251. Proteins - Transpath complexes
  252. Proteins - Transpath isogroups
  253. Proteins - Transpath modified forms
  254. Proteins - Transpath peptides
  255. Proteins - UniProt
  256. QUAST
  257. Quadratic Hill-climbing (analysis)
  258. Quality control analysis
  259. Quality control metrics (analysis)
  260. Quantification of RNA-seq in BAM format for mouse mm9 single end (workflow)
  261. Quantification of RNA-seq in FASTQ format for mouse mm9 single end (workflow)
  262. Quantification of RNA-seq with Cufflinks (no de-novo assembly) for FASTQ files (workflow)
  263. Quantification of RNA-seq with Cufflinks (with de-novo assembly) for FASTQ files (workflow)
  264. Quantification of RNA-seq with Cufflinks for multiple BAM files (workflow)
  265. Quantile normalization (analysis)
  266. Quasi-Steady-State Analysis
  267. Quasi-steady-state analysis example
  268. Query system (extension point)
  269. RADAU V
  270. RAGOUT
  271. RNA-Seq analysis
  272. ROC-curves in clusterized peaks (analysis)
  273. ROC-curves in grouped peaks (analysis)
  274. ROC-curves in overlapped ChIP-Seq peaks (analysis)
  275. ROC curves for best sites union (analysis)
  276. R (host object)
  277. R installation
  278. Rbiouml
  279. Reactions Analysis
  280. Reactome
  281. Read counter (analysis)
  282. Reads to matrices (workflow)
  283. Rebuild search indexes (analysis)
  284. Recalculate composite module score on new track (analysis)
  285. Recon transformer (analysis)
  286. Reduce CMA results (analysis)
  287. Reduce track (analysis)
  288. Reference type
  289. Reference type (extension point)
  290. Regression analysis
  291. Regression analysis advanced (analysis)
  292. Regulator search (analysis)
  293. Remote application client (analysis)
  294. Remove overlapping sites (analysis)
  295. Remove unobservable molecules (analysis)
  296. Report (analysis)
  297. Report (host object)
  298. Report generator for quality control analysis
  299. Repository
  300. Repository actions provider (extension point)
  301. Repository pane
  302. Repository pane toolbar
  303. Research diagram
  304. Ribo-Seq and mRNA features forming (analysis)
  305. RiboSeqExp (analysis)
  306. RiboseqArticleResult (analysis)
  307. Ru.biosoft.access.search (plugin)
  308. Ru.biosoft.access (plugin)
  309. Ru.biosoft.analysis.optimization (plugin)
  310. Ru.biosoft.analysis (plugin)
  311. Ru.biosoft.bsa.server (plugin)
  312. Ru.biosoft.bsa (plugin)
  313. Ru.biosoft.exception (plugin)
  314. Ru.biosoft.fs (plugin)
  315. Ru.biosoft.galaxy (plugin)
  316. Ru.biosoft.graph (plugin)
  317. Ru.biosoft.graphics (plugin)
  318. Ru.biosoft.jobcontrol (plugin)
  319. Ru.biosoft.math (plugin)
  320. Ru.biosoft.plugins.graph (plugin)
  321. Ru.biosoft.plugins.javascript (plugin)
  322. Ru.biosoft.plugins.jri (plugin)
  323. Ru.biosoft.proteome (plugin)
  324. Ru.biosoft.server.servlets (plugin)
  325. Ru.biosoft.server.tomcat (plugin)
  326. Ru.biosoft.server (plugin)
  327. Ru.biosoft.services (plugin)
  328. Ru.biosoft.table (plugin)
  329. Ru.biosoft.templates (plugin)
  330. Ru.biosoft.treetable (plugin)
  331. Ru.biosoft.vm (plugin)
  332. Ru.biosoft.workbench (plugin)
  333. Ru.biosoft.works (plugin)
  334. Run MACS 1.3.7 on ChiP-Seq (analysis)
  335. Run MACS 1.4.0 on ChiP-Seq (analysis)
  336. Run a Workflow as Analysis
  337. Run analysis
  338. SAM or BAM alignment file
  339. SBGN-ML (file format)
  340. SBGN examples
  341. SBGN extension
  342. SBML(CellDesigner) (file format)
  343. SBML (file format)
  344. SDE model (analysis)
  345. SDF file
  346. SED-ML file
  347. SEDX archive (file format)
  348. SEEK Synchronize (analysis)
  349. SIF (file format)
  350. SISSRs output (file format)
  351. SNP (reference type)
  352. SNP matching (analysis)
  353. SNP regions in genome (analysis)
  354. SNPs in binding regions (analysis)
  355. SPAdes
  356. SPAdes stats
  357. SRA to FASTQ (workflow)
  358. SVM (analysis)
  359. Sample population (analysis)
  360. Save hits (analysis)
  361. Save network (analysis)
  362. Sbml (host object)
  363. Sbw (host object)
  364. Score based FBC table builder (analysis)
  365. Script type (extension point)
  366. Script viewpart
  367. Search binding sites (analysis)
  368. Search for enriched TFBSs (genes) (analysis)
  369. Search for enriched TFBSs (tracks) (analysis)
  370. Search for self-regulating transcription factors (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  371. Search regulated genes (analysis)
  372. Search tools
  373. Select files from folder (analysis)
  374. Select keynodes with top targets (analysis)
  375. Select random rows (analysis)
  376. Select table columns (analysis)
  377. Select top rows (analysis)
  378. SelectionTrustClusters (analysis)
  379. Sensitivity Analysis
  380. Sensitivity analysis example
  381. Sequence (element type)
  382. Sequence mappability (analysis)
  383. Sequence minimal unique length (analysis)
  384. Server ICT
  385. Server administrator
  386. Servers
  387. Service (extension point)
  388. Set initial values from simulation result (analysis)
  389. Share molecules (analysis)
  390. Short term model of the heart output regulation
  391. Sign test (analysis)
  392. Simulate Population (analysis)
  393. Simulation
  394. SimulationEngine (host object)
  395. Simulation analysis
  396. SiteAnalysis (host object)
  397. Site Profile Filtering (analysis)
  398. Site Size Filtering (analysis)
  399. Site counts in repeats (analysis)
  400. Site distribution (analysis)
  401. Site model (element type)
  402. Site models - GTRD
  403. Site prediction
  404. Site search on gene set (analysis)
  405. Site search on track (analysis)
  406. Site search report (analysis)
  407. Site search result optimization (analysis)
  408. Site search summary (analysis)
  409. Sites Motifs Analysis
  410. Sites Open Chromatin Statistics (analysis)
  411. Sites Open Chromatin Statistics For Folders (analysis)
  412. Sites genome location (analysis)
  413. Sites genome location for folders (analysis)
  414. Softberry, Inc.
  415. Softberry (perspective)
  416. Solver (extension point)
  417. Sort SQL track (analysis)
  418. Split VCF by regulation (analysis)
  419. Split fasta (analysis)
  420. Steady State (analysis)
  421. Steady State Examples
  422. Stem-loop-miRNA - miRBase
  423. Stem loop predictor (analysis)
  424. Stoichiometric Matrix (analysis)
  425. Structures - PDB
  426. Stub process file (analysis)
  427. Substances (reference type)
  428. Substances - CAS
  429. Substances - ChEBI
  430. Substances - DrugBank
  431. Substances - DrugBank (geneXplain)
  432. Substances - KEGG
  433. Substances - Pharmaceutical compounds
  434. Summary on AUCs (analysis)
  435. Super annotate table (analysis)
  436. Systems biology - Get started
  437. Systems biology - basic model editing
  438. Systems biology - manual model construction
  439. Systems biology - model export
  440. Systems biology - model import
  441. Systems biology - model import 02
  442. Systems biology - model layout
  443. Systems biology - model simulation
  444. TF binding sites prediction in genome or track (analysis)
  445. TRANSFAC matrices format
  446. TRANSFAC profile (file format)
  447. TRRD
  448. Table (element type)
  449. Table (host object)
  450. Table document
  451. Table imputation (analysis)
  452. Tabular (file format)
  453. Template (extension point)
  454. Tests
  455. Text (element type)
  456. Text file
  457. Text output file generated by R (file format)
  458. Tools Comparison
  459. Tools Comparison 2022
  460. TrackInfo table creation (analysis)
  461. Track (element type)
  462. Track correlation (analysis)
  463. Track coverage (analysis)
  464. Track statistics (analysis)
  465. Track to gene set (analysis)
  466. Transcript set to track (analysis)
  467. Transcript structure analysis
  468. Transcriptome mappability (analysis)
  469. Transcriptome minimal unique length (analysis)
  470. Transcripts (reference type)
  471. Transcripts - Ensembl
  472. Transcripts - Illumina
  473. Transcripts - RefSeq
  474. Transform (host object)
  475. Transform table (analysis)
  476. Transform track to table (analysis)
  477. Transformer (extension point)
  478. Transplorer
  479. Treatment Simulation (analysis)
  480. Tree-table (element type)
  481. Tree-table document
  482. TreeMap on Functional classification (analysis)
  483. Tutorials
  484. Two multivariate sample analysis
  485. Type driver (extension point)
  486. Types (extension point)
  487. Univariate sample analysis
  488. Univariate samples analysis
  489. Unspecified (reference type)
  490. Up and Down Identification (analysis)
  491. Update master track (analysis)
  492. Update pubmed (analysis)
  493. Upload from FTP (analysis)
  494. Upstream analysis (TRANSFAC(R) and GeneWays) (workflow)
  495. Upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  496. Upstream analysis with feedback loop (TRANSFAC(R) and TRANSPATH(R)) (workflow)
  497. to user communication
  498. Using Galaxy in BioUML
  499. Using R in BioUML
  500. VAT output (file format)

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