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- Probes - Affymetrix ST (3 revisions)
- Infer network (analysis) (3 revisions)
- Blast alignment coverage (analysis) (3 revisions)
- Report generator for quality control analysis (3 revisions)
- ArticleComparator (analysis) (3 revisions)
- Genes (reference type) (3 revisions)
- Transcript structure analysis (3 revisions)
- Download model (analysis) (3 revisions)
- Isoform TE (analysis) (3 revisions)
- Merge peaks (analysis) (3 revisions)
- Convert diagram to Transpath (analysis) (3 revisions)
- Proteins - PDB (3 revisions)
- Illumina metylation probes to track (analysis) (3 revisions)
- Reference type (3 revisions)
- Find gene fusions from RNA-seq (workflow) (3 revisions)
- 1-dimensional arterial tree model (3 revisions)
- Group table rows (analysis) (3 revisions)
- Find miRNA feed forward loops with CMA (analysis) (3 revisions)
- Matrices (reference type) (3 revisions)
- ArticleTrackCreator (analysis) (3 revisions)
- Optimization document (3 revisions)
- Genes - BKL (3 revisions)
- Transcriptome mappability (analysis) (3 revisions)
- Drugs - DrugBank (3 revisions)
- Identification of cis-regulatory modules with given pattern of TF-classes (analysis) (3 revisions)
- Make GTF for riboseq alignment (analysis) (3 revisions)
- Merge simulation results (analysis) (3 revisions)
- Select keynodes with top targets (analysis) (3 revisions)
- Analyze any DNA sequence, EMBL (workflow) (3 revisions)
- Convert diagram to pairs (analysis) (3 revisions)
- Create miRNA promoters (analysis) (3 revisions)
- Treatment Simulation (analysis) (3 revisions)
- Quality control analysis (3 revisions)
- Reference type (extension point) (3 revisions)
- KeyNodes hub (3 revisions)
- Find genome variants and indels from RNA-seq (workflow) (3 revisions)
- Categories - ExPASy (3 revisions)
- Cis-module sets near given genes (analysis) (3 revisions)
- 3D viewer (3 revisions)
- Server administrator (3 revisions)
- Copy data element (analysis) (3 revisions)
- Find regulatory regions (analysis) (3 revisions)
- ChIP-Seq - Identify and classify target genes (TRANSPATH(R)) (workflow) (3 revisions)
- Score based FBC table builder (analysis) (3 revisions)
- Site search report (analysis) (3 revisions)
- Transcriptome minimal unique length (analysis) (3 revisions)
- Identification of composite elements by filters (analysis) (3 revisions)
- JVODE (3 revisions)
- Merge table columns (analysis) (3 revisions)
- Select random rows (analysis) (3 revisions)
- Analyze any DNA sequence, Fasta (workflow) (3 revisions)
- Convert files to tracks (analysis) (3 revisions)
- Sort SQL track (analysis) (3 revisions)
- Quality control metrics (analysis) (3 revisions)
- Regression analysis (3 revisions)
- Find genome variants and indels from full-genome NGS (workflow) (3 revisions)
- SNPs in binding regions (analysis) (3 revisions)
- MicroRNA finder (analysis) (3 revisions)
- Compute differentially expressed genes (Agilent Tox probes) (workflow) (3 revisions)
- SiteAnalysis (host object) (3 revisions)
- Perspective (extension point) (3 revisions)
- Bsa (host object) (3 revisions)
- Matrices - TRANSFAC (3 revisions)
- Construct composite modules on track (correlation) (analysis) (3 revisions)
- BAM filter multi-hits (analysis) (3 revisions)
- DataFilter (host object) (3 revisions)
- Proteins (reference type) (3 revisions)
- Transcripts (reference type) (3 revisions)
- Visible plugin (extension point) (3 revisions)
- Filtration of predicted sites by filters (analysis) (3 revisions)
- CRISPR Cas9 and specific oligonucleotides (analysis) (3 revisions)
- Analyze any DNA sequence, GeneBank (workflow) (3 revisions)
- Convert genomic BAM to transcriptomic (analysis) (3 revisions)
- Split VCF by regulation (analysis) (3 revisions)
- Probes (reference type) (3 revisions)
- Proteins - Transfac (3 revisions)
- Update pubmed (analysis) (3 revisions)
- Regression analysis advanced (analysis) (3 revisions)
- Find longest connected chains (analysis) (3 revisions)
- Install Reactome (analysis) (3 revisions)
- Find shortest path between two sets (analysis) (3 revisions)
- Collaborative diagram editing (3 revisions)
- Algebraic steady state (analysis) (3 revisions)
- BAM filter strand specific (analysis) (3 revisions)
- Prediction of TF-binding sites of given TF (analysis) (3 revisions)
- Proteins - BKL (3 revisions)
- Identify enriched composite modules in promoters (GTRD) (workflow) (3 revisions)
- CR cluster selector (analysis) (3 revisions)
- Map Transfac sites to genome (analysis) (3 revisions)
- Ftp (host object) (3 revisions)
- Change diagram (analysis) (3 revisions)
- Compare TFBS mutations (analysis) (3 revisions)
- Select top rows (analysis) (3 revisions)
- Convert identifiers for multiple gene sets (workflow) (3 revisions)
- Split fasta (analysis) (3 revisions)
- Proteins - Transpath (3 revisions)
- TreeMap on Functional classification (analysis) (3 revisions)
- GTRD analysis (3 revisions)
- Classification analysis advanced (analysis) (3 revisions)
- Set initial values from simulation result (analysis) (3 revisions)
- Pharmaceutical Compounds analysis (3 revisions)
- Docker meta (3 revisions)
- Fastx clip (3 revisions)
- Colon cancer signature2 (analysis) (3 revisions)
- Prediction of miRNA binding sites (workflow) (3 revisions)
- Proteins - EndoNet (3 revisions)
- Transcripts - Illumina (3 revisions)
- Hypergeometric analysis for multiple inputs (workflow) (3 revisions)
- Reads to matrices (workflow) (3 revisions)
- SelectionTrustClusters (analysis) (3 revisions)
- Table imputation (analysis) (3 revisions)
- Proteins - Transpath complexes (3 revisions)
- Quantification of RNA-seq with Cufflinks (no de-novo assembly) for FASTQ files (workflow) (3 revisions)
- LS-regression analysis (3 revisions)
- Mapping to ontology - select a classification (2 Gene tables) (workflow) (3 revisions)
- GTRD analysis advanced (analysis) (3 revisions)
- Classification hub (3 revisions)
- SRA to FASTQ (workflow) (3 revisions)
- Share molecules (analysis) (3 revisions)
- Antimony (file format) (3 revisions)
- BioUML installation (3 revisions)
- Track correlation (analysis) (3 revisions)
- Ribo-Seq and mRNA features forming (analysis) (3 revisions)
- Find unmappable regions (analysis) (3 revisions)
- Moved class (extension point) (3 revisions)
- Genes - Illumina (3 revisions)
- Find common effectors for multiple gene sets (GeneWays) (workflow) (3 revisions)
- Mappability histogram (analysis) (3 revisions)
- SEDX archive (file format) (3 revisions)
- Analyze any DNA sequence for site enrichment (GTRD) (workflow) (3 revisions)
- Convert site search summary (analysis) (3 revisions)
- Create profile from site model table (analysis) (3 revisions)
- Two multivariate sample analysis (3 revisions)
- Quantification of RNA-seq with Cufflinks (with de-novo assembly) for FASTQ files (workflow) (3 revisions)
- Import HOCOMOCO (analysis) (3 revisions)
- Mapping to ontology - select a classification (Gene table) (workflow) (3 revisions)
- SVM (analysis) (3 revisions)
- Model (host object) (3 revisions)
- Short term model of the heart output regulation (3 revisions)
- Application log (viewpart) (3 revisions)
- Open per TF view (analysis) (3 revisions)
- Plot2D (analysis) (3 revisions)
- Encode quality metrics estimation (analysis) (3 revisions)
- RiboSeqExp (analysis) (3 revisions)
- FinderArticlePoints (analysis) (3 revisions)
- Color space to nucleotide (analysis) (3 revisions)
- Biohub (host object) (3 revisions)
- Genes - Transpath (3 revisions)
- Biouml.plugins.genomeenhancer (plugin) (3 revisions)
- Proteins - GTRD (3 revisions)
- Transform (host object) (3 revisions)
- Proteins - Transpath modified forms (3 revisions)
- Identify enriched motifs in promoters (TRANSFAC(R)) (workflow) (3 revisions)
- Estimate read density (analysis) (3 revisions)
- Mapping to GO ontologies and comparison for two gene sets (workflow) (3 revisions)
- Functional classification by diagrams (analysis) (3 revisions)
- SEEK Synchronize (analysis) (3 revisions)
- Diagram graph compare analysis (3 revisions)
- Quantification of RNA-seq with Cufflinks for multiple BAM files (workflow) (3 revisions)
- Upstream analysis with feedback loop (TRANSFAC(R) and TRANSPATH(R)) (workflow) (3 revisions)
- Import ensembl homology (analysis) (3 revisions)
- Extract RNA length (analysis) (3 revisions)
- Remove unobservable molecules (analysis) (3 revisions)
- Large sequence minimal unique length (analysis) (3 revisions)
- Cell type specific TFBS prediction (3 revisions)
- Mapping to ontology - select a classification (Multiple Gene tables) (workflow) (3 revisions)
- CloudBioLinux (3 revisions)
- Sign test (analysis) (3 revisions)
- CoverageCheker (analysis) (3 revisions)
- Plot bar chart (analysis) (3 revisions)
- DDMoRe consortium (3 revisions)
- Enhance Score (analysis) (3 revisions)
- CMA Result Statistic (analysis) (3 revisions)
- RiboseqArticleResult (analysis) (3 revisions)
- ChIP-seq Quality control analysis (3 revisions)
- Com.developmentontheedge.beans (plugin) (3 revisions)
- Analysis of Binding Regions (analysis) (3 revisions)
- Beans (extension point) (3 revisions)
- Create flat files (analysis) (3 revisions)
- Prepare cluster to exp table (analysis) (3 revisions)
- Databases installation (3 revisions)
- Transform table (analysis) (3 revisions)
- Proteins - Transpath peptides (3 revisions)
- Euler (3 revisions)
- Recon transformer (analysis) (3 revisions)
- Calculate keynodes ranks (analysis) (3 revisions)
- Method description HTML file (3 revisions)
- ComputeProfileSums (analysis) (3 revisions)
- Sequence (element type) (3 revisions)
- Peak finders comparison (analysis) (3 revisions)
- Stem loop predictor (analysis) (3 revisions)
- Create state (analysis) (3 revisions)
- Biouml.plugins.ccsignature (plugin) (3 revisions)
- Diagram to user hub collection (analysis) (3 revisions)
- Import from BC Platform (analysis) (2 revisions)
- Simulate Population (analysis) (2 revisions)
- GWAS format (2 revisions)
- Coverage Profiles Cutoff (analysis) (2 revisions)
- DNase-seq Group and Profile Generation (Previous version) (analysis) (2 revisions)
- Product (2 revisions)
- Enriched upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow) (2 revisions)
- Intersect tracks (analysis) (2 revisions)
- Search regulated genes (analysis) (2 revisions)
- Sites genome location for folders (analysis) (2 revisions)
- Geneways (2 revisions)
- Default (perspective) (2 revisions)
- Transform track to table (analysis) (2 revisions)
- Univariate sample analysis (2 revisions)
- Identify enriched motifs in tissue specific tracks (TRANSFAC(R)) (workflow) (2 revisions)
- Join two tables (analysis) (2 revisions)
- Calculate weighted mutation score (analysis) (2 revisions)
- Ru.biosoft.jobcontrol (plugin) (2 revisions)
- Mapping to ontologies (HumanPSD(TM)) (workflow) (2 revisions)
- ChromatinInfo table creation (analysis) (2 revisions)
- Methylation probes - Illumina (2 revisions)
- Create tissue-specific promoter track (analysis) (2 revisions)
- Probes - Affymetrix RaGene-2-0-st (2 revisions)
- Text (element type) (2 revisions)
- Using Galaxy in BioUML (2 revisions)
- Import from TranSMART (analysis) (2 revisions)
- Bioumlsim (2 revisions)
- Limma (analysis) (2 revisions)
- Galaxy (2 revisions)
- DNase-seq Group and Profile Generation (analysis) (2 revisions)
- Profile (element type) (2 revisions)
- IPython format (2 revisions)
- R (host object) (2 revisions)
- MSAT (analysis) (2 revisions)
- Prepare target genes by expression (analysis) (2 revisions)
- Proteins - NCBI (2 revisions)
- Transformer (extension point) (2 revisions)
- Univariate samples analysis (2 revisions)
- Identify enriched motifs in tracks (TRANSFAC(R)) (workflow) (2 revisions)
- Reduce track (analysis) (2 revisions)
- Find enriched TF binding sites in variation sites (TRANSFAC(R)) (workflow) (2 revisions)
- Categories (reference type) (2 revisions)
- MiRNA - miRBase (2 revisions)
- Compute coverage by window (analysis) (2 revisions)
- Gene set enrichment analysis HumanPSD (Affymetrix probes) (workflow) (2 revisions)
- Create transcript region track (analysis) (2 revisions)
- Biouml.plugins.machinelearning (plugin) (2 revisions)
- Using R in BioUML (2 revisions)
- Fast table filter (analysis) (2 revisions)
- Find master regulators in networks with context genes (TRANSPATH(R)) (workflow) (2 revisions)
- Sbml (host object) (2 revisions)
- Affymetrix CEL file (2 revisions)
- SimulationEngine (host object) (2 revisions)
- Optimization (host object) (2 revisions)
- Galaxy (host object) (2 revisions)
- Profiles Statistics (analysis) (2 revisions)
- COVID-19 parameters for Lung (2 revisions)
- Focused upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow) (2 revisions)
- Select files from folder (analysis) (2 revisions)
- Softberry (perspective) (2 revisions)
- Create matrix logo (analysis) (2 revisions)
- KEGG (reference type) (2 revisions)
- Categories - BKL (2 revisions)
- Mapping to ontologies and comparison for two gene sets (HumanPSD(TM)) (workflow) (2 revisions)
- GTEX Mutation effect on sites (analysis) (2 revisions)
- MiRNA feed forward loops (analysis) (2 revisions)
- Compute coverage profile (analysis) (2 revisions)
- Normalization quality plots (analysis) (2 revisions)
- Convert tracks to VCF (analysis) (2 revisions)
- BioUML Simulation result (file format) (2 revisions)
- Perfectosape (host object) (2 revisions)
- Stub process file (analysis) (2 revisions)
- Gene set enrichment analysis HumanPSD (Agilent probes) (workflow) (2 revisions)
- Probes - Affymetrix miRNA-1-0 (2 revisions)
- Biouml.plugins.pathfinder (plugin) (2 revisions)
- ChIP-Seq - Identify and classify target genes (HumanPSD(TM)) (workflow) (2 revisions)
- Sbw (host object) (2 revisions)
- Galaxy admin (2 revisions)
- Systems biology - basic model editing (2 revisions)
- Virtual physiological human (2 revisions)
- COVID-19 parameters for Nasopharynx (2 revisions)
- Mutation effect on sites advanced (analysis) (2 revisions)
- BioGears (2 revisions)
- Preprocessor (extension point) (2 revisions)
- TRRD viewer (2 revisions - redirect page)
- Genome browser (2 revisions)
- Illumina microarray file (2 revisions)
- Mapping to ontologies and comparison for two gene sets (TRANSPATH(R)) (workflow) (2 revisions)
- SNP regions in genome (analysis) (2 revisions)
- Substances (reference type) (2 revisions)
- Gene set enrichment analysis HumanPSD (Gene table) (workflow) (2 revisions)
- Probes - Affymetrix miRNA-2-0 (2 revisions)
- Guided linear model analysis (2 revisions)
- Biouml.plugins.metabolics (plugin) (2 revisions)
- Fastq compressed (file format) (2 revisions)
- Agilent microarray file (2 revisions)
- Population generation (analysis) (2 revisions)
- Das (host object) (2 revisions)
- EBarrays (analysis) (2 revisions)
- Ensembl (host object) (2 revisions)
- Filtering experiments by cell types (analysis) (2 revisions)
- Mutations to genes with weights (analysis) (2 revisions)
- BioHub (2 revisions)
- Create per TF flat files (analysis) (2 revisions)
- Tree-table (element type) (2 revisions)
- Update master track (analysis) (2 revisions)
- Export master track (analysis) (2 revisions)
- Mapping to ontologies for multiple gene sets (HumanPSD(TM)) (workflow) (2 revisions)
- GTRD (perspective) (2 revisions)
- Cistrom construction (analysis) (2 revisions)
- AUC Estimation For meta-cluster track (analysis) (2 revisions)
- Servers (2 revisions)
- Normalize Affymetrix experiment and control (analysis) (2 revisions)
- Substances - CAS (2 revisions)
- Gene set enrichment analysis HumanPSD (Illumina probes) (workflow) (2 revisions)
- Cross-species identification of enriched motifs in promoters, using orthologue information (TRANSFAC(R)) (workflow) (2 revisions)
- Probes - Affymetrix miRNA-3-0 (2 revisions)
- Install HumanPSD(TM) database (analysis) (2 revisions)
- Find regulatory regions with mutations (analysis) (2 revisions)
- Identify composite modules in promoters (TRANSFAC(R)) (workflow) (2 revisions)
- Reactome (2 revisions)
- ChIP experiment - GTRD (2 revisions)
- Create profile from CMA model (analysis) (2 revisions)
- Table (host object) (2 revisions)
- Tree-table document (2 revisions)
- Quantification of RNA-seq in BAM format for mouse mm9 single end (workflow) (2 revisions)
- Export metadata json (analysis) (2 revisions)
- Categories - Gene ontology (2 revisions)
- Microarray (host object) (2 revisions)
- Service (extension point) (2 revisions)
- Normalize Agilent experiment and control (analysis) (2 revisions)
- Site Profile Filtering (analysis) (2 revisions)
- PharmML (2 revisions)
- Cross-species mapping to ontologies, using orthologue information (HumanPSD(TM)) (workflow) (2 revisions)
- Probes - Affymetrix miRNA-4-0 (2 revisions)
- TrackInfo table creation (analysis) (2 revisions)
- Variance filter (analysis) (2 revisions)
- Galaxy method (element type) (2 revisions)
- Find 10 master regulators in networks (TRANSPATH(R)) (workflow) (2 revisions)
- Ru.biosoft.exception (plugin) (2 revisions)
- Pathways (reference type) (2 revisions)
- Get miRNA targets (analysis) (2 revisions)
- Quantification of RNA-seq in FASTQ format for mouse mm9 single end (workflow) (2 revisions)
- Export per cell clusters (analysis) (2 revisions)
- LRPath (analysis) (2 revisions)
- Cdk (host object) (2 revisions)
- Normalize Illumina experiment and control (analysis) (2 revisions)
- Site Size Filtering (analysis) (2 revisions)
- Substances - DrugBank (2 revisions)
- Biouml.plugins.cytoscape (plugin) (2 revisions)
- Track (element type) (2 revisions)
- RNA-Seq analysis (2 revisions)
- Research diagram (2 revisions)
- Look and feel (extension point) (2 revisions)
- Find target genes (analysis) (2 revisions)
- Construct composite modules on tracks (without site search) (analysis) (2 revisions)
- Outer join (analysis) (2 revisions)
- Sites Motifs Analysis (2 revisions)
- Systems biology - model import 02 (2 revisions)
- Identify enriched composite modules in promoters (TRANSFAC(R)) (workflow) (2 revisions)
- Enzymes - ExPASy (2 revisions)
- Biouml.plugins.seek (plugin) (2 revisions)
- Find 3 master regulators in networks with context genes (TRANSPATH(R)) (workflow) (2 revisions)
- Compare analysis results (analysis) (2 revisions)
- Analyze any DNA sequence (TRANSFAC(R)) (workflow) (2 revisions)
- Network (host object) (2 revisions)
- BioPAX file (2 revisions)
- Create profile from matrix library (analysis) (2 revisions)
- Probes - Affymetrix HG-U133+ PM (2 revisions)
- Biouml.plugins.mirprom (plugin) (2 revisions)
- Remote application client (analysis) (2 revisions)
- ModelReduction (host object) (2 revisions)
- Oligonucleotides in sequence samples (analysis) (2 revisions)
- Substances - DrugBank (geneXplain) (2 revisions)
- General control panel (2 revisions)
- Cytoscape network format (2 revisions)
- Probes - Agilent Tox Array (2 revisions)
- Element type (2 revisions)
- Matrix derivation (analysis) (2 revisions)
- Colon cancer signature (analysis) (2 revisions)
- Search for enriched TFBSs (genes) (analysis) (2 revisions)
- Sites Open Chromatin Statistics (analysis) (2 revisions)
- Create custom project (analysis) (2 revisions)
- Systems biology - model layout (2 revisions)
- Data matrix operations (analysis) (2 revisions)
- IPS-scores in SNPs (analysis) (2 revisions)
- Enzymes - KEGG (2 revisions)
- Calculate CMA regulation (analysis) (2 revisions)
- Check Workflow consistency (analysis) (2 revisions)
- Probes - Affymetrix HTA-2-0 (2 revisions)
- Proteins - Transpath isogroups (2 revisions)
- Find master regulators in mutated network (TRANSPATH(R)) (workflow) (2 revisions)
- Clean up SQL database (analysis) (2 revisions)
- Add calculated column (analysis) (2 revisions)
- Substances - KEGG (2 revisions)
- Generate Table From JSON (analysis) (2 revisions)
- DAE Models examples (2 revisions)
- Heatmap (analysis) (2 revisions)
- Document pane (2 revisions)
- Verify Condition for Table (analysis) (2 revisions)
- Run analysis (2 revisions)
- Search for enriched TFBSs (tracks) (analysis) (2 revisions)
- Multivariate regression analysis (2 revisions)
- BPMN (2 revisions)
- Sites Open Chromatin Statistics For Folders (analysis) (2 revisions)
- Find common effectors for multiple gene sets (TRANSPATH(R)) (workflow) (2 revisions)
- Calculate TFs regulatory score (analysis) (2 revisions)
- Check quotas (analysis) (2 revisions)
- Node (host object) (2 revisions)
- Stem-loop-miRNA - miRBase (2 revisions)
- Create random track (analysis) (2 revisions)
- Probes - Affymetrix HuGene-2-0-st (2 revisions)
- GlycanR (analysis) (2 revisions)
- Find master regulators in mutated network (workflow) (2 revisions)
- Model analysis (2 revisions)
- Open regulated genes table (analysis) (2 revisions)
- Substances - Pharmaceutical compounds (2 revisions)
- Intersect tables (analysis) (2 revisions)
- Filter SPAdes output (2 revisions)
- MEALR (tracks) (analysis) (2 revisions)
- Flux Balance Analysis (workflow) (2 revisions)
- Mature-miRNA - miRBase (2 revisions)
- Search for self-regulating transcription factors (TRANSFAC(R) and TRANSPATH(R)) (workflow) (2 revisions)
- Multivariate sample analysis (2 revisions)
- Context item (extension point) (2 revisions)
- PCA (analysis) (2 revisions)
- Sites genome location (analysis) (2 revisions)
- TF binding sites prediction in genome or track (analysis) (2 revisions)
- Identify enriched motifs in tissue specific promoters (TRANSFAC(R)) (workflow) (2 revisions)
- Wizard page (extension point) (2 revisions)
- Chipmunk (host object) (2 revisions)
- Analyze miRNA target enrichment (analysis) (2 revisions)
- Convert table to VCF track (analysis) (2 revisions)
- Probes - Affymetrix HuGene-2-1-st (2 revisions)
