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- Functional classification by diagrams (analysis) (1,512 bytes) (fully protected) (Protection log)
- Create flat files (analysis) (570 bytes) (fully protected) (Protection log)
- SEEK Synchronize (analysis) (727 bytes) (fully protected) (Protection log)
- Match genes and metabolites (analysis) (910 bytes) (fully protected) (Protection log)
- Join GTRD clusters (analysis) (774 bytes) (fully protected) (Protection log)
- Make meta tracks (analysis) (732 bytes) (fully protected) (Protection log)
- Merge peak callers (analysis) (690 bytes) (fully protected) (Protection log)
- Merge peaks (analysis) (817 bytes) (fully protected) (Protection log)
- Prepare cluster to exp table (analysis) (658 bytes) (fully protected) (Protection log)
- Open tracks for all TF (analysis) (753 bytes) (fully protected) (Protection log)
- Open per TF view (analysis) (546 bytes) (fully protected) (Protection log)
- Cluster by path (analysis) (1,193 bytes) (fully protected) (Protection log)
- Simulate Population (analysis) (704 bytes) (fully protected) (Protection log)
- Find longest connected chains (analysis) (2,312 bytes) (fully protected) (Protection log)
- BAM filter strand specific (analysis) (1,030 bytes) (fully protected) (Protection log)
- Sample population (analysis) (2,977 bytes) (fully protected) (Protection log)
- Find shortest path between two sets (analysis) (1,620 bytes) (fully protected) (Protection log)
- ComputeProfileSums (analysis) (1,350 bytes) (fully protected) (Protection log)
- Convert genomic BAM to transcriptomic (analysis) (1,174 bytes) (fully protected) (Protection log)
- Estimate read density (analysis) (1,425 bytes) (fully protected) (Protection log)
- Large sequence minimal unique length (analysis) (795 bytes) (fully protected) (Protection log)
- Transcript structure analysis (882 bytes) (fully protected) (Protection log)
- Find unmappable regions (analysis) (848 bytes) (fully protected) (Protection log)
- Make GTF for riboseq alignment (analysis) (1,146 bytes) (fully protected) (Protection log)
- Sequence minimal unique length (analysis) (737 bytes) (fully protected) (Protection log)
- Isoform TE (analysis) (1,334 bytes) (fully protected) (Protection log)
- Transcriptome mappability (analysis) (1,544 bytes) (fully protected) (Protection log)
- Plot2D (analysis) (555 bytes) (fully protected) (Protection log)
- Report (analysis) (562 bytes) (fully protected) (Protection log)
- Transcriptome minimal unique length (analysis) (1,116 bytes) (fully protected) (Protection log)
- Sequence mappability (analysis) (1,057 bytes) (fully protected) (Protection log)
- Flux Balance Analysis (workflow) (747 bytes) (fully protected) (Protection log)
- Hypergeometric analysis for multiple inputs (workflow) (2,376 bytes) (fully protected) (Protection log)
- Quantification of RNA-seq in BAM format for mouse mm9 single end (workflow) (402 bytes) (fully protected) (Protection log)
- Quantification of RNA-seq in FASTQ format for mouse mm9 single end (workflow) (410 bytes) (fully protected) (Protection log)
- Identify enriched composite modules in promoters (GTRD) (workflow) (2,040 bytes) (fully protected) (Protection log)
- Identify enriched motifs in tissue specific tracks (TRANSFAC(R)) (workflow) (807 bytes) (fully protected) (Protection log)
- Find master regulators in networks with context genes (TRANSPATH(R)) (workflow) (1,651 bytes) (fully protected) (Protection log)
- Identify enriched motifs in tissue specific promoters (TRANSFAC(R)) (workflow) (804 bytes) (fully protected) (Protection log)
- Cross-species identification of enriched motifs in promoters, using orthologue information (TRANSFAC(R)) (workflow) (646 bytes) (fully protected) (Protection log)
- Find 10 master regulators in networks (TRANSPATH(R)) (workflow) (1,520 bytes) (fully protected) (Protection log)
- Find master regulators in mutated network (workflow) (370 bytes) (fully protected) (Protection log)
- Find 3 master regulators in networks with context genes (TRANSPATH(R)) (workflow) (1,571 bytes) (fully protected) (Protection log)
- Focused upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow) (550 bytes) (fully protected) (Protection log)
- Upstream analysis with feedback loop (TRANSFAC(R) and TRANSPATH(R)) (workflow) (2,899 bytes) (fully protected) (Protection log)
- Search for self-regulating transcription factors (TRANSFAC(R) and TRANSPATH(R)) (workflow) (596 bytes) (fully protected) (Protection log)
- Biouml.plugins.ccsignature (plugin) (1,014 bytes) (fully protected) (Protection log)
- Biouml.plugins.metabolics (plugin) (497 bytes) (fully protected) (Protection log)
- Biouml.plugins.genomeenhancer (plugin) (2,086 bytes) (fully protected) (Protection log)
- Com.developmentontheedge.beans (plugin) (178 bytes) (fully protected) (Protection log)
- Biouml.plugins.seek (plugin) (345 bytes) (fully protected) (Protection log)
- Category:Colon cancer signature (analyses group) (104 bytes) (fully protected) (Protection log)
- Category:Biosoft analyses (88 bytes) (fully protected) (Protection log)
- Category:Population (analyses group) (92 bytes) (fully protected) (Protection log)
- Category:Biosoft plugins (86 bytes) (fully protected) (Protection log)
- Drugs - DrugBank (305 bytes) (fully protected) (Protection log)
- Categories - BKL (308 bytes) (fully protected) (Protection log)
- Substances - Pharmaceutical compounds (464 bytes) (fully protected) (Protection log)
- Substances - DrugBank (geneXplain) (474 bytes) (fully protected) (Protection log)
- Mature-miRNA - miRBase (305 bytes) (fully protected) (Protection log)
- Stem-loop-miRNA - miRBase (312 bytes) (fully protected) (Protection log)
- Methylation probes - Illumina (433 bytes) (fully protected) (Protection log)
- Probes - Affymetrix HTA-2-0 (565 bytes) (fully protected) (Protection log)
- Install Reactome (analysis) (706 bytes) (fully protected) (Protection log)
- CMA Result Statistic (analysis) (671 bytes) (fully protected) (Protection log)
- Construct composite modules on track (correlation) (analysis) (2,921 bytes) (fully protected) (Protection log)
- Continue CMA (analysis) (2,835 bytes) (fully protected) (Protection log)
- Create miRNA promoters (analysis) (795 bytes) (fully protected) (Protection log)
- Find miRNA feed forward loops with CMA (analysis) (976 bytes) (fully protected) (Protection log)
- Illumina metylation probes to track (analysis) (679 bytes) (fully protected) (Protection log)
- Reduce CMA results (analysis) (1,122 bytes) (fully protected) (Protection log)
- Sort SQL track (analysis) (555 bytes) (fully protected) (Protection log)
- Track correlation (analysis) (626 bytes) (fully protected) (Protection log)
- Data matrix operations (analysis) (1,260 bytes) (fully protected) (Protection log)
- Fantom analysis (1,754 bytes) (fully protected) (Protection log)
- GTRD analysis (5,577 bytes) (fully protected) (Protection log)
- GTRD analysis advanced (analysis) (1,468 bytes) (fully protected) (Protection log)
- CR cluster selector (analysis) (818 bytes) (fully protected) (Protection log)
- Merge table columns (analysis) (859 bytes) (fully protected) (Protection log)
- Plot bar chart (analysis) (1,021 bytes) (fully protected) (Protection log)
- Plot pie chart (analysis) (801 bytes) (fully protected) (Protection log)
- Plot scatter chart (analysis) (815 bytes) (fully protected) (Protection log)
- Select random rows (analysis) (682 bytes) (fully protected) (Protection log)
- Select top rows (analysis) (1,178 bytes) (fully protected) (Protection log)
- Super annotate table (analysis) (746 bytes) (fully protected) (Protection log)
- Transform table (analysis) (696 bytes) (fully protected) (Protection log)
- TreeMap on Functional classification (analysis) (1,083 bytes) (fully protected) (Protection log)
- ChIP-seq Quality control analysis (2,155 bytes) (fully protected) (Protection log)
- Encode quality metrics estimation (analysis) (487 bytes) (fully protected) (Protection log)
- Prepare finished tables (analysis) (549 bytes) (fully protected) (Protection log)
- Quality control analysis (1,826 bytes) (fully protected) (Protection log)
- Quality control metrics (analysis) (1,202 bytes) (fully protected) (Protection log)
- Report generator for quality control analysis (2,096 bytes) (fully protected) (Protection log)
- Update pubmed (analysis) (435 bytes) (fully protected) (Protection log)
- Calculate TFs regulatory score (analysis) (790 bytes) (fully protected) (Protection log)
- Find regulatory regions (analysis) (2,022 bytes) (fully protected) (Protection log)
- Calculate keynodes ranks (analysis) (1,784 bytes) (fully protected) (Protection log)
- Generate workflow from annotation diagram (analysis) (2,529 bytes) (fully protected) (Protection log)
- PSD pharmaceutical compounds analysis (1,308 bytes) (fully protected) (Protection log)
- Pharmaceutical Compounds analysis (1,969 bytes) (fully protected) (Protection log)
- Select keynodes with top targets (analysis) (1,819 bytes) (fully protected) (Protection log)
- Split VCF by regulation (analysis) (1,023 bytes) (fully protected) (Protection log)
- Cytoscape network format (512 bytes) (fully protected) (Protection log)
- Classification analysis advanced (analysis) (3,143 bytes) (fully protected) (Protection log)
- Regression analysis advanced (analysis) (4,180 bytes) (fully protected) (Protection log)
- Convert diagram to Transpath (analysis) (881 bytes) (fully protected) (Protection log)
- Convert diagram to pairs (analysis) (785 bytes) (fully protected) (Protection log)
- Diagram to user hub collection (analysis) (778 bytes) (fully protected) (Protection log)
- Enhance Score (analysis) (702 bytes) (fully protected) (Protection log)
- Infer network (analysis) (521 bytes) (fully protected) (Protection log)
- Treatment Simulation (analysis) (2,786 bytes) (fully protected) (Protection log)
- Mappability histogram (analysis) (735 bytes) (fully protected) (Protection log)
- Quantile normalization (analysis) (1,046 bytes) (fully protected) (Protection log)
- Table imputation (analysis) (705 bytes) (fully protected) (Protection log)
- Sign test (analysis) (733 bytes) (fully protected) (Protection log)
- ChIP-Seq - Identify and classify target genes (HumanPSD(TM)) (workflow) (689 bytes) (fully protected) (Protection log)
- Cross-species mapping to ontologies, using orthologue information (HumanPSD(TM)) (workflow) (600 bytes) (fully protected) (Protection log)
- Gene set enrichment analysis HumanPSD (Affymetrix probes) (workflow) (1,610 bytes) (fully protected) (Protection log)
- Gene set enrichment analysis HumanPSD (Agilent probes) (workflow) (1,814 bytes) (fully protected) (Protection log)
- Gene set enrichment analysis HumanPSD (Gene table) (workflow) (1,330 bytes) (fully protected) (Protection log)
- Gene set enrichment analysis HumanPSD (Illumina probes) (workflow) (1,602 bytes) (fully protected) (Protection log)
- Mapping to ontologies (HumanPSD(TM)) (workflow) (497 bytes) (fully protected) (Protection log)
- Mapping to ontologies and comparison for two gene sets (HumanPSD(TM)) (workflow) (407 bytes) (fully protected) (Protection log)
- Mapping to ontologies for multiple gene sets (HumanPSD(TM)) (workflow) (1,637 bytes) (fully protected) (Protection log)
- Find master regulators in mutated network (TRANSPATH(R)) (workflow) (397 bytes) (fully protected) (Protection log)
- Ru.biosoft.jobcontrol (plugin) (162 bytes) (fully protected) (Protection log)
- Ru.biosoft.exception (plugin) (166 bytes) (fully protected) (Protection log)
- Biouml.plugins.pathfinder (plugin) (287 bytes) (fully protected) (Protection log)
- Biouml.plugins.mirprom (plugin) (364 bytes) (fully protected) (Protection log)
- Biouml.plugins.machinelearning (plugin) (493 bytes) (fully protected) (Protection log)
- Biouml.plugins.cytoscape (plugin) (348 bytes) (fully protected) (Protection log)
- Category:Genome enhancer (analyses group) (97 bytes) (fully protected) (Protection log)
- Category:Machine learning (analyses group) (98 bytes) (fully protected) (Protection log)
- Convert tracks to VCF (analysis) (806 bytes) (fully protected) (Protection log)
- Install HumanPSD(TM) database (analysis) (659 bytes) (fully protected) (Protection log)
- Analyze miRNA target enrichment (analysis) (1,686 bytes) (fully protected) (Protection log)
- Create matrix logo (analysis) (1,199 bytes) (fully protected) (Protection log)
- Create profile from matrix library (analysis) (1,134 bytes) (fully protected) (Protection log)
- Get miRNA targets (analysis) (716 bytes) (fully protected) (Protection log)
- MEALR (tracks) (analysis) (1,874 bytes) (fully protected) (Protection log)
- MSAT (analysis) (1,738 bytes) (fully protected) (Protection log)
- Search for enriched TFBSs (genes) (analysis) (4,505 bytes) (fully protected) (Protection log)
- Search for enriched TFBSs (tracks) (analysis) (4,605 bytes) (fully protected) (Protection log)
- Cistrom construction (analysis) (1,773 bytes) (fully protected) (Protection log)
- RNA-Seq analysis (1,860 bytes) (fully protected) (Protection log)
- Construct composite modules on tracks (without site search) (analysis) (3,253 bytes) (fully protected) (Protection log)
- Create random track (analysis) (2,093 bytes) (fully protected) (Protection log)
- Create tissue-specific promoter track (analysis) (1,296 bytes) (fully protected) (Protection log)
- Create transcript region track (analysis) (2,039 bytes) (fully protected) (Protection log)
- Import from BC Platform (analysis) (903 bytes) (fully protected) (Protection log)
- Import from TranSMART (analysis) (900 bytes) (fully protected) (Protection log)
- Intersect tables (analysis) (1,192 bytes) (fully protected) (Protection log)
- Intersect tracks (analysis) (1,569 bytes) (fully protected) (Protection log)
- Normalization quality plots (analysis) (1,222 bytes) (fully protected) (Protection log)
- Normalize Affymetrix experiment and control (analysis) (1,948 bytes) (fully protected) (Protection log)
- Normalize Agilent experiment and control (analysis) (1,823 bytes) (fully protected) (Protection log)
- Normalize Illumina experiment and control (analysis) (2,171 bytes) (fully protected) (Protection log)
- Outer join (analysis) (1,156 bytes) (fully protected) (Protection log)
- MiRNA feed forward loops (analysis) (3,002 bytes) (fully protected) (Protection log)
- Model analysis (621 bytes) (fully protected) (Protection log)
- GTEX Mutation effect on sites (analysis) (1,773 bytes) (fully protected) (Protection log)
- Filtering experiments by cell types (analysis) (1,001 bytes) (fully protected) (Protection log)
- Mutation effect on sites advanced (analysis) (2,175 bytes) (fully protected) (Protection log)
- Open regulated genes table (analysis) (735 bytes) (fully protected) (Protection log)
- Search regulated genes (analysis) (1,029 bytes) (fully protected) (Protection log)
- Site Size Filtering (analysis) (613 bytes) (fully protected) (Protection log)
- AUC Estimation For meta-cluster track (analysis) (1,244 bytes) (fully protected) (Protection log)
- ChromatinInfo table creation (analysis) (552 bytes) (fully protected) (Protection log)
- Coverage Profiles Cutoff (analysis) (617 bytes) (fully protected) (Protection log)
- Create per TF flat files (analysis) (434 bytes) (fully protected) (Protection log)
- DNase-seq Group and Profile Generation (analysis) (756 bytes) (fully protected) (Protection log)
- DNase-seq Group and Profile Generation (Previous version) (analysis) (762 bytes) (fully protected) (Protection log)
- Export master track (analysis) (695 bytes) (fully protected) (Protection log)
- Export metadata json (analysis) (621 bytes) (fully protected) (Protection log)
- Export per cell clusters (analysis) (496 bytes) (fully protected) (Protection log)
- Find target genes (analysis) (839 bytes) (fully protected) (Protection log)
- Prepare target genes by expression (analysis) (456 bytes) (fully protected) (Protection log)
- Profiles Statistics (analysis) (1,417 bytes) (fully protected) (Protection log)
- Site Profile Filtering (analysis) (635 bytes) (fully protected) (Protection log)
- Sites Motifs Analysis (2,006 bytes) (fully protected) (Protection log)
- Sites Open Chromatin Statistics (analysis) (1,173 bytes) (fully protected) (Protection log)
- Sites Open Chromatin Statistics For Folders (analysis) (1,049 bytes) (fully protected) (Protection log)
- Sites genome location (analysis) (1,628 bytes) (fully protected) (Protection log)
- Sites genome location for folders (analysis) (1,385 bytes) (fully protected) (Protection log)
- TrackInfo table creation (analysis) (540 bytes) (fully protected) (Protection log)
- Update master track (analysis) (1,215 bytes) (fully protected) (Protection log)
- Calculate CMA regulation (analysis) (1,780 bytes) (fully protected) (Protection log)
- Calculate weighted mutation score (analysis) (1,757 bytes) (fully protected) (Protection log)
- Create profile from CMA model (analysis) (754 bytes) (fully protected) (Protection log)
- Fast table filter (analysis) (741 bytes) (fully protected) (Protection log)
- Find regulatory regions with mutations (analysis) (2,006 bytes) (fully protected) (Protection log)
- Mutations to genes with weights (analysis) (1,525 bytes) (fully protected) (Protection log)
- Verify Condition for Table (analysis) (799 bytes) (fully protected) (Protection log)
- Affymetrix CEL file (451 bytes) (fully protected) (Protection log)
- Agilent microarray file (385 bytes) (fully protected) (Protection log)
- BioUML Simulation result (file format) (378 bytes) (fully protected) (Protection log)
- Fastq compressed (file format) (467 bytes) (fully protected) (Protection log)
- GWAS format (1,066 bytes) (fully protected) (Protection log)
- IPython format (536 bytes) (fully protected) (Protection log)
- Illumina microarray file (390 bytes) (fully protected) (Protection log)
- Compute coverage by window (analysis) (1,214 bytes) (fully protected) (Protection log)
- Compute coverage profile (analysis) (781 bytes) (fully protected) (Protection log)
- Convert table to VCF track (analysis) (1,429 bytes) (fully protected) (Protection log)
- Reduce track (analysis) (942 bytes) (fully protected) (Protection log)
- Population generation (analysis) (6,041 bytes) (fully protected) (Protection log)
- Compare analysis results (analysis) (1,318 bytes) (fully protected) (Protection log)
- EBarrays (analysis) (4,232 bytes) (fully protected) (Protection log)
- GlycanR (analysis) (1,133 bytes) (fully protected) (Protection log)
- Guided linear model analysis (5,596 bytes) (fully protected) (Protection log)
- Heatmap (analysis) (2,419 bytes) (fully protected) (Protection log)
- LRPath (analysis) (2,270 bytes) (fully protected) (Protection log)
- Limma (analysis) (3,321 bytes) (fully protected) (Protection log)
- PCA (analysis) (2,096 bytes) (fully protected) (Protection log)
- Variance filter (analysis) (847 bytes) (fully protected) (Protection log)
- TF binding sites prediction in genome or track (analysis) (1,572 bytes) (fully protected) (Protection log)
- Add calculated column (analysis) (1,283 bytes) (fully protected) (Protection log)
- Join two tables (analysis) (2,081 bytes) (fully protected) (Protection log)
- Generate Table From JSON (analysis) (544 bytes) (fully protected) (Protection log)
- Run analysis (573 bytes) (fully protected) (Protection log)
- Select files from folder (analysis) (642 bytes) (fully protected) (Protection log)
- Stub process file (analysis) (565 bytes) (fully protected) (Protection log)
- Check Workflow consistency (analysis) (640 bytes) (fully protected) (Protection log)
- Remote application client (analysis) (500 bytes) (fully protected) (Protection log)
- Category:ChIP-seq (analyses group) (90 bytes) (fully protected) (Protection log)
- Category:Composite module analyses (analyses group) (107 bytes) (fully protected) (Protection log)
- Category:Differential algebraic equations (analyses group) (114 bytes) (fully protected) (Protection log)
- Category:GTEX (analyses group) (86 bytes) (fully protected) (Protection log)
- Category:GTRD build (analyses group) (92 bytes) (fully protected) (Protection log)
- Category:Gene models (analyses group) (93 bytes) (fully protected) (Protection log)
- Category:Gene set analysis (analyses group) (99 bytes) (fully protected) (Protection log)
- Category:Match sites and genes (analyses group) (103 bytes) (fully protected) (Protection log)
- Category:MicroRNA (analyses group) (90 bytes) (fully protected) (Protection log)
- Category:Microarray normalization (analyses group) (106 bytes) (fully protected) (Protection log)
- Category:Motif discovery (analyses group) (97 bytes) (fully protected) (Protection log)
- Category:Mutations (analyses group) (91 bytes) (fully protected) (Protection log)
- Category:NGS color-space (analyses group) (97 bytes) (fully protected) (Protection log)
- Category:NGS utils (analyses group) (91 bytes) (fully protected) (Protection log)
- Category:Operations with genomic tracks (analyses group) (112 bytes) (fully protected) (Protection log)
- Category:Parameter fitting (analyses group) (99 bytes) (fully protected) (Protection log)
- Category:Plots and charts (analyses group) (98 bytes) (fully protected) (Protection log)
- Category:RNA-seq (analyses group) (89 bytes) (fully protected) (Protection log)
- Category:Ribosome profiling (analyses group) (100 bytes) (fully protected) (Protection log)
- Category:SEDML (analyses group) (87 bytes) (fully protected) (Protection log)
- Category:Sequence mappability (analyses group) (102 bytes) (fully protected) (Protection log)
- Category:TF binding site search (analyses group) (104 bytes) (fully protected) (Protection log)
- Category:Table manipulation (analyses group) (100 bytes) (fully protected) (Protection log)
- Category:Trash (analyses group) (87 bytes) (fully protected) (Protection log)
- Category:Unclassified (analyses group) (94 bytes) (fully protected) (Protection log)
- Category:Workflow utils (analyses group) (96 bytes) (fully protected) (Protection log)
- Category:MiRNA (analyses group) (87 bytes) (fully protected) (Protection log)