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Pindel output (file format)Plot2D (analysis)Plot bar chart (analysis)
Plot pie chart (analysis)Plot scatter chart (analysis)Plugin development
Polynomial Regression analysisPopulation 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)
PresentationsProbes (reference type)Probes - Affymetrix
Probes - Affymetrix HG-U133+ PMProbes - Affymetrix HTA-2-0Probes - Affymetrix HuGene-2-0-st
Probes - Affymetrix HuGene-2-1-stProbes - Affymetrix RaGene-2-0-stProbes - Affymetrix ST
Probes - Affymetrix miRNA-1-0Probes - Affymetrix miRNA-2-0Probes - Affymetrix miRNA-3-0
Probes - Affymetrix miRNA-4-0Probes - AgilentProbes - Agilent Tox Array
Probes - IlluminaProcess track with sites (analysis)Product
Profile (element type)Profiles Statistics (analysis)Project
Proteins (reference type)Proteins - BKL
Proteins - EndoNetProteins - EnsemblProteins - GTRD
Proteins - GenBankProteins - IPIProteins - NCBI
Proteins - PDBProteins - ReactomeProteins - RefSeq
Proteins - TransfacProteins - TranspathProteins - Transpath complexes
Proteins - Transpath isogroupsProteins - Transpath modified formsProteins - Transpath peptides
Proteins - UniProtQUASTQuadratic Hill-climbing (analysis)
Quality control analysisQuality 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 exampleQuery system (extension point)
RADAU VRAGOUTRNA-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
RbioumlReactions AnalysisReactome
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 typeReference type (extension point)
Regression analysisRegression 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
RepositoryRepository actions provider (extension point)Repository pane
Repository pane toolbarResearch diagramRibo-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 AnalysisRun analysis
SAM or BAM alignment fileSBGN-ML (file format)SBGN examples
SBGN extensionSBML(CellDesigner) (file format)SBML (file format)
SDE model (analysis)SDF fileSED-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 statsSRA 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 viewpartSearch 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 toolsSelect 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 exampleSequence (element type)Sequence mappability (analysis)
Sequence minimal unique length (analysis)Server ICTServer administrator
ServersService (extension point)Set initial values from simulation result (analysis)
Share molecules (analysis)Short term model of the heart output regulationSign test (analysis)
Simulate Population (analysis)SimulationSimulationEngine (host object)
Simulation analysisSiteAnalysis (host object)Site Profile Filtering (analysis)
Site Size Filtering (analysis)Site counts in repeats (analysis)Site distribution (analysis)
Site model (element type)Site models - GTRDSite 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 - miRBaseStem loop predictor (analysis)Stoichiometric Matrix (analysis)
Structures - PDBStub process file (analysis)Substances (reference type)
Substances - CASSubstances - ChEBISubstances - DrugBank
Substances - DrugBank (geneXplain)Substances - KEGGSubstances - Pharmaceutical compounds
Summary on AUCs (analysis)Super annotate table (analysis)Systems biology - Get started
Systems biology - basic model editingSystems biology - manual model constructionSystems biology - model export
Systems biology - model importSystems biology - model import 02Systems biology - model layout
Systems biology - model simulationTF 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)
TestsText (element type)Text file
Text output file generated by R (file format)Tools ComparisonTools 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 analysisTranscriptome mappability (analysis)
Transcriptome minimal unique length (analysis)Transcripts (reference type)Transcripts - Ensembl
Transcripts - IlluminaTranscripts - RefSeqTransform (host object)
Transform table (analysis)Transform track to table (analysis)Transformer (extension point)
TransplorerTreatment Simulation (analysis)Tree-table (element type)
Tree-table documentTreeMap on Functional classification (analysis)Tutorials
Two multivariate sample analysisType driver (extension point)Types (extension point)
Univariate sample analysisUnivariate samples analysisUnspecified (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 communicationUsing Galaxy in BioUML
Using R in BioUMLVAT output (file format)VCF format
Validate Experiments (analysis)Variance filter (analysis)Varscan output (file format)
Venn diagrams (analysis)Verify Condition for Table (analysis)Viewpart
Virtual biologyVirtual collection (extension point)
Virtual physiological humanVirtual ratVisible plugin (extension point)
Visual modelingVisualize results (analysis)Westerhoff and Kolodkin 2020 COVID19 model
Wiggle formatWizard page (extension point)Workflow
ZIP-archive (file format)Моделирование сердечно-сосудистой системы
Оptimization documentСистема кровообращения человека

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