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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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