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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	Projects	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	Quasy-steady-state approximation
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
TRRD viewer	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)
VCF format	Validate Experiments (analysis)	Variance filter (analysis)
Varscan output (file format)	Venn diagrams (analysis)	Verify Condition for Table (analysis)
Viewpart	Viewparts	Virtual biology
Virtual collection (extension point)	Virtual physiological human	Virtual rat
Visible plugin (extension point)	Visual modeling	Visualize results (analysis)
Westerhoff and Kolodkin 2020 COVID19 model	Wiggle format	Wizard page (extension point)
Workflow	Workflows	ZIP-archive (file format)

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