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- Get transcripts track (analysis)
- GinSim (file format)
- GlycanR (analysis)
- Glycan structures
- Graph search
- Grid layout
- Group table rows (analysis)
- Guided linear model analysis
- HTML file
- Hadoop
- Hash parameters
- Headless BioUML
- Heatmap (analysis)
- Hemodynamics model (file format)
- Heterozygous site caller (analysis)
- Hierarchical layout
- Hormone - EndoNet
- Host object (extension point)
- Html (element type)
- HumanSim
- Hypergeometric analysis
- Hypergeometric analysis for multiple inputs (workflow)
- IPS-scores in SNPs (analysis)
- IPS ROC-curves (analysis)
- IPS motif discovery (analysis)
- IPS prediction (analysis)
- IPython format
- Identical best site ROC-curves (analysis)
- Identification of cis-regulatory modules with given pattern of TF-classes (analysis)
- Identification of composite elements by filters (analysis)
- Identify composite modules in promoters (TRANSFAC(R)) (workflow)
- Identify enriched composite modules in promoters (GTRD) (workflow)
- Identify enriched composite modules in promoters (TRANSFAC(R)) (workflow)
- Identify enriched motifs in promoters (GTRD) (workflow)
- Identify enriched motifs in promoters (TRANSFAC(R)) (workflow)
- Identify enriched motifs in tissue specific promoters (TRANSFAC(R)) (workflow)
- Identify enriched motifs in tissue specific tracks (TRANSFAC(R)) (workflow)
- Identify enriched motifs in tracks (TRANSFAC(R)) (workflow)
- Illumina metylation probes to track (analysis)
- Illumina microarray file
- Illumina normalization (analysis)
- Image (element type)
- Image file
- Import (extension point)
- Import HOCOMOCO (analysis)
- Import ensembl homology (analysis)
- Import from BC Platform (analysis)
- Import from TranSMART (analysis)
- Infer network (analysis)
- Information box
- Install ExPASy (analysis)
- Install HumanPSD(TM) database (analysis)
- Install Reactome (analysis)
- Install TRANSFAC(R) database (analysis)
- Install TRANSPATH(R) database (analysis)
- Institute of Systems Biology
- Intersect tables (analysis)
- Intersect tracks (analysis)
- Interval format
- Isoform TE (analysis)
- Isoforms - GTRD
- JVODE
- Join GTRD Tracks (analysis)
- Join GTRD clusters (analysis)
- Join diagrams (analysis)
- Join several tables (analysis)
- Join table (analysis)
- Join tracks (analysis)
- Join two tables (analysis)
- Jupyter
- KEGG (reference type)
- KeyNodes hub
- Key Node Sensitivity Analysis
- Kinetic parameters for COVID-19 models
- LRPath (analysis)
- LS-regression analysis
- Landing
- Large sequence minimal unique length (analysis)
- Layout (extension point)
- Limma (analysis)
- LincRNA and mRNA features (analysis)
- Linear Shifted Model (analysis)
- Locations of best sites (analysis)
- Long-term model of the CVS/Renal system
- Look and feel (extension point)
- Lucene indexes creation
- MEALR (tracks) (analysis)
- MGL
- MSAT (analysis)
- Make GTF for riboseq alignment (analysis)
- Make meta tracks (analysis)
- Manual parameter fitting
- Map Transfac sites to genome (analysis)
- Map to Transpath (analysis)
- Mappability histogram (analysis)
- Mapping to GO ontologies and comparison for two gene sets (workflow)
- Mapping to ontologies (Gene table) (workflow)
- Mapping to ontologies (HumanPSD(TM)) (workflow)
- Mapping to ontologies (TRANSPATH(R)) (workflow)
- Mapping to ontologies and comparison for two gene sets (HumanPSD(TM)) (workflow)
- Mapping to ontologies and comparison for two gene sets (TRANSPATH(R)) (workflow)
- Mapping to ontologies for multiple gene sets (HumanPSD(TM)) (workflow)
- Mapping to ontologies for multiple gene sets (TRANSPATH(R)) (workflow)
- Mapping to ontologies for multiple gene sets (workflow)
- Mapping to ontology - select a classification (2 Gene tables) (workflow)
- Mapping to ontology - select a classification (Gene table) (workflow)
- Mapping to ontology - select a classification (Multiple Gene tables) (workflow)
- Mass Conservation Analysis
- Match genes and metabolites (analysis)
- Matching BioHub
- Matrices (reference type)
- Matrices - GTRD
- Matrices - TRANSFAC
- Matrix (element type)
- Matrix comparison (analysis)
- Matrix derivation (analysis)
- Matrix library (element type)
- Mature-miRNA - miRBase
- Merge binding regions for cell-lines (analysis)
- Merge peak callers (analysis)
- Merge peaks (analysis)
- Merge simulation results (analysis)
- Merge table columns (analysis)
- Merge track statistics (analysis)
- Meta analysis
- Metabolic Control Analysis
- Metabolic control analysis example
- Method (extension point)
- Method description HTML file
- Methylation probes - Illumina
- MiRNA - miRBase
- MiRNA feed forward loops (analysis)
- MicroRNA aligner (analysis)
- MicroRNA finder (analysis)
- Microarray (host object)
- Mixture of normal components (analysis)
- ModelReduction (host object)
- Model (host object)
- Model analysis
- Modeling Antihypertensive drugs
- Modeling cardiovascular system
- Modular model of the human CVS v.1
- Modular model of the human CVS v.2
- Modular modeling
- Module type (extension point)
- Motif quality analysis
- Moved class (extension point)
- Multivariate regression analysis
- Multivariate sample analysis
- Muscle metabolism
- Mutation effect (analysis)
- Mutation effect on sites (analysis)
- Mutation effect on sites advanced (analysis)
- Mutations to genes with weights (analysis)
- N-Glycan biosynthesis
- NGS misc
- Network (host object)
- New BioStore
- Node (host object)
- Non-Linear Mixed Effects Model
- Non-merged ChIP-Seq tracks summary (analysis)
- Nonlinear Model (analysis)
- Normalization quality plots (analysis)
- Normalize (host object)
- Normalize Affymetrix experiment and control (analysis)
- Normalize Agilent experiment and control (analysis)
- Normalize Illumina experiment and control (analysis)
- Oligonucleotides in sequence samples (analysis)
- Open per TF view (analysis)
- Open regulated genes table (analysis)
- Open tracks for all TF (analysis)
- Optimization (host object)
- Optimization document
- Optimization examples
- Optimization problem
- Orthogonal layout
- Outer join (analysis)
- Overall circulation model
- PASS analysis
- PCA (analysis)
- PSD pharmaceutical compounds analysis
- Parameter fitting (analysis)
- Parameter identifiability (optimization) (analysis)
- Parameter identifiability (table) (analysis)
- Parameter identifiability example
- Particle swarm optimization (analysis)
- Pathways (reference type)
- Pathways - Reactome
- Pathways - Transpath
- Patient-specific cardiovascular model
- Peak finders comparison (analysis)
- Peaks to matrices (workflow)
- Perfectosape (analysis)
- Perfectosape (host object)
- Perspective
- Perspective (extension point)
- PharmML
- Pharmaceutical Compounds analysis
- Pindel output (file format)
- Plot2D (analysis)
- Plot bar chart (analysis)
- Plot pie chart (analysis)
- Plot scatter chart (analysis)
- Plugin development
- Polynomial Regression analysis
- Population generation (analysis)
- PredictStartSites (analysis)
- Prediction of TF-binding sites of given TF (analysis)
- Prediction of miRNA binding sites (workflow)
- Prepare GTF annotation (analysis)
- Prepare Search by regulation (analysis)
- Prepare cluster to exp table (analysis)
- Prepare finished tables (analysis)
- Prepare target genes by expression (analysis)
- Preprocess raw reads (analysis)
- Preprocessor (extension point)
- Presentations
- Probes (reference type)
- Probes - Affymetrix
- Probes - Affymetrix HG-U133+ PM
- Probes - Affymetrix HTA-2-0
- Probes - Affymetrix HuGene-2-0-st
- Probes - Affymetrix HuGene-2-1-st
- Probes - Affymetrix RaGene-2-0-st
- Probes - Affymetrix ST
- Probes - Affymetrix miRNA-1-0
- Probes - Affymetrix miRNA-2-0
- Probes - Affymetrix miRNA-3-0
- Probes - Affymetrix miRNA-4-0
- Probes - Agilent
- Probes - Agilent Tox Array
- Probes - Illumina
- Process track with sites (analysis)
- Product
- Profile (element type)
- Profiles Statistics (analysis)
- Project
- Proteins (reference type)
- Proteins - BKL
- Proteins - EndoNet
- Proteins - Ensembl
- Proteins - GTRD
- Proteins - GenBank
- Proteins - IPI
- Proteins - NCBI
- Proteins - PDB
- Proteins - Reactome
- Proteins - RefSeq
- Proteins - Transfac
- Proteins - Transpath
- Proteins - Transpath complexes
- Proteins - Transpath isogroups
- Proteins - Transpath modified forms
- Proteins - Transpath peptides
- Proteins - UniProt
- QUAST
- Quadratic Hill-climbing (analysis)
- Quality control analysis
- Quality control metrics (analysis)
- Quantification of RNA-seq in BAM format for mouse mm9 single end (workflow)
- Quantification of RNA-seq in FASTQ format for mouse mm9 single end (workflow)
- Quantification of RNA-seq with Cufflinks (no de-novo assembly) for FASTQ files (workflow)
- Quantification of RNA-seq with Cufflinks (with de-novo assembly) for FASTQ files (workflow)
- Quantification of RNA-seq with Cufflinks for multiple BAM files (workflow)
- Quantile normalization (analysis)
- Quasi-Steady-State Analysis
- Quasi-steady-state analysis example
- Query system (extension point)
- RADAU V
- RAGOUT
- RNA-Seq analysis
- ROC-curves in clusterized peaks (analysis)
- ROC-curves in grouped peaks (analysis)
- ROC-curves in overlapped ChIP-Seq peaks (analysis)
- ROC curves for best sites union (analysis)
- R (host object)
- R installation
- Rbiouml
- Reactions Analysis
- Reactome
- Read counter (analysis)
- Reads to matrices (workflow)
- Rebuild search indexes (analysis)
- Recalculate composite module score on new track (analysis)
- Recon transformer (analysis)
- Reduce CMA results (analysis)
- Reduce track (analysis)
- Reference type
- Reference type (extension point)
- Regression analysis
- Regression analysis advanced (analysis)
- Regulator search (analysis)
- Remote application client (analysis)
- Remove overlapping sites (analysis)
- Remove unobservable molecules (analysis)
- Report (analysis)
- Report (host object)
- Report generator for quality control analysis
- Repository
- Repository actions provider (extension point)
- Repository pane
- Repository pane toolbar
- Research diagram
- Ribo-Seq and mRNA features forming (analysis)
- RiboSeqExp (analysis)
- RiboseqArticleResult (analysis)
- Ru.biosoft.access.search (plugin)
- Ru.biosoft.access (plugin)
- Ru.biosoft.analysis.optimization (plugin)
- Ru.biosoft.analysis (plugin)
- Ru.biosoft.bsa.server (plugin)
- Ru.biosoft.bsa (plugin)
- Ru.biosoft.exception (plugin)
- Ru.biosoft.fs (plugin)
- Ru.biosoft.galaxy (plugin)
- Ru.biosoft.graph (plugin)
- Ru.biosoft.graphics (plugin)
- Ru.biosoft.jobcontrol (plugin)
- Ru.biosoft.math (plugin)
- Ru.biosoft.plugins.graph (plugin)
- Ru.biosoft.plugins.javascript (plugin)
- Ru.biosoft.plugins.jri (plugin)
- Ru.biosoft.proteome (plugin)
- Ru.biosoft.server.servlets (plugin)
- Ru.biosoft.server.tomcat (plugin)
- Ru.biosoft.server (plugin)
- Ru.biosoft.services (plugin)
- Ru.biosoft.table (plugin)
- Ru.biosoft.templates (plugin)
- Ru.biosoft.treetable (plugin)
- Ru.biosoft.vm (plugin)
- Ru.biosoft.workbench (plugin)
- Ru.biosoft.works (plugin)
- Run MACS 1.3.7 on ChiP-Seq (analysis)
- Run MACS 1.4.0 on ChiP-Seq (analysis)
- Run a Workflow as Analysis
- Run analysis
- SAM or BAM alignment file
- SBGN-ML (file format)
- SBGN examples
- SBGN extension
- SBML(CellDesigner) (file format)
- SBML (file format)
- SDE model (analysis)
- SDF file
- SED-ML file
- SEDX archive (file format)
- SEEK Synchronize (analysis)
- SIF (file format)
- SISSRs output (file format)
- SNP (reference type)
- SNP matching (analysis)
- SNP regions in genome (analysis)
- SNPs in binding regions (analysis)
- SPAdes
- SPAdes stats
- SRA to FASTQ (workflow)
- SVM (analysis)
- Sample population (analysis)
- Save hits (analysis)
- Save network (analysis)
- Sbml (host object)
- Sbw (host object)
- Score based FBC table builder (analysis)
- Script type (extension point)
- Script viewpart
- Search binding sites (analysis)
- Search for enriched TFBSs (genes) (analysis)
- Search for enriched TFBSs (tracks) (analysis)
- Search for self-regulating transcription factors (TRANSFAC(R) and TRANSPATH(R)) (workflow)
- Search regulated genes (analysis)
- Search tools
- Select files from folder (analysis)
- Select keynodes with top targets (analysis)
- Select random rows (analysis)
- Select table columns (analysis)
- Select top rows (analysis)
- SelectionTrustClusters (analysis)
- Sensitivity Analysis
- Sensitivity analysis example
- Sequence (element type)
- Sequence mappability (analysis)
- Sequence minimal unique length (analysis)
- Server ICT
- Server administrator
- Servers
- Service (extension point)
- Set initial values from simulation result (analysis)
- Share molecules (analysis)
- Short term model of the heart output regulation
- Sign test (analysis)
- Simulate Population (analysis)
- Simulation
- SimulationEngine (host object)
- Simulation analysis
- SiteAnalysis (host object)
- Site Profile Filtering (analysis)
- Site Size Filtering (analysis)
- Site counts in repeats (analysis)
- Site distribution (analysis)
- Site model (element type)
- Site models - GTRD
- Site prediction
- Site search on gene set (analysis)
- Site search on track (analysis)
- Site search report (analysis)
- Site search result optimization (analysis)
- Site search summary (analysis)
- Sites Motifs Analysis
- Sites Open Chromatin Statistics (analysis)
- Sites Open Chromatin Statistics For Folders (analysis)
- Sites genome location (analysis)
- Sites genome location for folders (analysis)
- Softberry, Inc.
- Softberry (perspective)
- Solver (extension point)
- Sort SQL track (analysis)
- Split VCF by regulation (analysis)
- Split fasta (analysis)
- Steady State (analysis)
- Steady State Examples
- Stem-loop-miRNA - miRBase
- Stem loop predictor (analysis)
- Stoichiometric Matrix (analysis)
- Structures - PDB
- Stub process file (analysis)
- Substances (reference type)
- Substances - CAS
- Substances - ChEBI
- Substances - DrugBank
- Substances - DrugBank (geneXplain)
- Substances - KEGG
- Substances - Pharmaceutical compounds
- Summary on AUCs (analysis)
- Super annotate table (analysis)
- Systems biology - Get started
- Systems biology - basic model editing
- Systems biology - manual model construction
- Systems biology - model export
- Systems biology - model import
- Systems biology - model import 02
- Systems biology - model layout
- Systems biology - model simulation
- TF binding sites prediction in genome or track (analysis)
- TRANSFAC matrices format
- TRANSFAC profile (file format)
- TRRD
- Table (element type)
- Table (host object)
- Table document
- Table imputation (analysis)
- Tabular (file format)
- Template (extension point)
- Tests
- Text (element type)
- Text file
- Text output file generated by R (file format)
- Tools Comparison
- Tools Comparison 2022
- TrackInfo table creation (analysis)
- Track (element type)
- Track correlation (analysis)
- Track coverage (analysis)
- Track statistics (analysis)
- Track to gene set (analysis)
- Transcript set to track (analysis)
- Transcript structure analysis
- Transcriptome mappability (analysis)
- Transcriptome minimal unique length (analysis)
- Transcripts (reference type)
- Transcripts - Ensembl
- Transcripts - Illumina
- Transcripts - RefSeq
- Transform (host object)
- Transform table (analysis)
- Transform track to table (analysis)
- Transformer (extension point)
- Transplorer
- Treatment Simulation (analysis)
- Tree-table (element type)
- Tree-table document
- TreeMap on Functional classification (analysis)
- Tutorials
- Two multivariate sample analysis
- Type driver (extension point)
- Types (extension point)
- Univariate sample analysis
- Univariate samples analysis
- Unspecified (reference type)
- Up and Down Identification (analysis)
- Update master track (analysis)
- Update pubmed (analysis)
- Upload from FTP (analysis)
- Upstream analysis (TRANSFAC(R) and GeneWays) (workflow)
- Upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)
- Upstream analysis with feedback loop (TRANSFAC(R) and TRANSPATH(R)) (workflow)
- to user communication
- Using Galaxy in BioUML
- Using R in BioUML
- VAT output (file format)