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Folder (element type)	Force directed layout	Ftp (host object)
Function (extension point)	Functional classification (analysis)	Functional classification by diagrams (analysis)
GC island finder (analysis)	GLBSOLVE (analysis)	GO installation
GTEX Mutation effect on sites (analysis)	GTRD	GTRD (perspective)
GTRD Workflow	GTRD analysis	GTRD analysis advanced (analysis)
GTRD comparison	GTRD statistics	GWAS format
Galaxy	Galaxy (host object)	Galaxy admin
Galaxy cloud	Galaxy installation	Galaxy method (element type)
Gathering genome statistics (analysis)	GenBank format	GeneNet
GeneXplain	GeneXplain GmbH	Gene Ontology
Gene Ontology database	Gene Transfer Format	Gene expression prediction
Gene features (analysis)	Gene overlap statistics (analysis)	Gene set enrichment analysis (Affymetrix probes) (workflow)
Gene set enrichment analysis (Agilent probes) (workflow)	Gene set enrichment analysis (Gene table) (workflow)	Gene set enrichment analysis (Illumina probes) (workflow)
Gene set enrichment analysis - select a classification (Gene table) (workflow)	Gene set enrichment analysis HumanPSD (Affymetrix probes) (workflow)	Gene set enrichment analysis HumanPSD (Agilent probes) (workflow)
Gene set enrichment analysis HumanPSD (Gene table) (workflow)	Gene set enrichment analysis HumanPSD (Illumina probes) (workflow)	Gene set to track (analysis)
General Feature Format	General control panel	Generate Table From JSON (analysis)
Generate dynamic model (analysis)	Generate workflow from annotation diagram (analysis)	Generic file
Genes (reference type)	Genes - BKL	Genes - Ensembl
Genes - Entrez	Genes - GenBank	Genes - Gene symbol
Genes - Illumina	Genes - Transpath	Genes - Unigene
Geneways	Genome Browser iframe	Genome Browser json
Genome browser	Genome browser iframe	Genome coverage (analysis)
Get miRNA targets (analysis)	Get transcripts track (analysis)	GinSim (file format)
GlycanR (analysis)	Glycan structures	Graph search
Grid layout	Group table rows (analysis)	Guided linear model analysis
HTML file	Hadoop	Hash parameters
Headless BioUML	Heatmap (analysis)	Hemodynamics model (file format)
Heterozygous site caller (analysis)	Hierarchical layout	Hormone - EndoNet
Host object (extension point)	Html (element type)	HumanSim
Hypergeometric analysis	Hypergeometric analysis for multiple inputs (workflow)	IPS-scores in SNPs (analysis)
IPS ROC-curves (analysis)	IPS motif discovery (analysis)	IPS prediction (analysis)
IPython format	Identical best site ROC-curves (analysis)	Identification of cis-regulatory modules with given pattern of TF-classes (analysis)
Identification of composite elements by filters (analysis)	Identify composite modules in promoters (TRANSFAC(R)) (workflow)	Identify enriched composite modules in promoters (GTRD) (workflow)
Identify enriched composite modules in promoters (TRANSFAC(R)) (workflow)	Identify enriched motifs in promoters (GTRD) (workflow)	Identify enriched motifs in promoters (TRANSFAC(R)) (workflow)
Identify enriched motifs in tissue specific promoters (TRANSFAC(R)) (workflow)	Identify enriched motifs in tissue specific tracks (TRANSFAC(R)) (workflow)	Identify enriched motifs in tracks (TRANSFAC(R)) (workflow)
Illumina metylation probes to track (analysis)	Illumina microarray file	Illumina normalization (analysis)
Image (element type)	Image file	Import (extension point)
Import HOCOMOCO (analysis)	Import ensembl homology (analysis)	Import from BC Platform (analysis)
Import from TranSMART (analysis)	Infer network (analysis)	Information box
Install ExPASy (analysis)	Install HumanPSD(TM) database (analysis)	Install Reactome (analysis)
Install TRANSFAC(R) database (analysis)	Install TRANSPATH(R) database (analysis)	Institute of Systems Biology
Intersect tables (analysis)	Intersect tracks (analysis)	Interval format
Isoform TE (analysis)	Isoforms - GTRD	JVODE
Join GTRD Tracks (analysis)	Join GTRD clusters (analysis)	Join diagrams (analysis)
Join several tables (analysis)	Join table (analysis)	Join tracks (analysis)
Join two tables (analysis)	Jupyter	KEGG (reference type)
KeyNodes hub	Key Node Sensitivity Analysis	Kinetic parameters for COVID-19 models
LRPath (analysis)	LS-regression analysis	Landing
Large sequence minimal unique length (analysis)	Layout (extension point)	Limma (analysis)
LincRNA and mRNA features (analysis)	Linear Shifted Model (analysis)	Locations of best sites (analysis)
Logical track	Long-term model of the CVS/Renal system	Look and feel (extension point)
Lucene indexes creation	Lucene search	MEALR (tracks) (analysis)
MGL	MSAT (analysis)	Main Page
Make GTF for riboseq alignment (analysis)	Make meta tracks (analysis)	Manual parameter fitting
Map Transfac sites to genome (analysis)	Map to Transpath (analysis)	Mappability histogram (analysis)
Mapping to GO ontologies and comparison for two gene sets (workflow)	Mapping to ontologies (Gene table) (workflow)	Mapping to ontologies (HumanPSD(TM)) (workflow)
Mapping to ontologies (TRANSPATH(R)) (workflow)	Mapping to ontologies and comparison for two gene sets (HumanPSD(TM)) (workflow)	Mapping to ontologies and comparison for two gene sets (TRANSPATH(R)) (workflow)
Mapping to ontologies for multiple gene sets (HumanPSD(TM)) (workflow)	Mapping to ontologies for multiple gene sets (TRANSPATH(R)) (workflow)	Mapping to ontologies for multiple gene sets (workflow)
Mapping to ontology - select a classification (2 Gene tables) (workflow)	Mapping to ontology - select a classification (Gene table) (workflow)	Mapping to ontology - select a classification (Multiple Gene tables) (workflow)
Mass Conservation Analysis	Match genes and metabolites (analysis)	Matching BioHub
Matrices (reference type)	Matrices - GTRD	Matrices - TRANSFAC
Matrix (element type)	Matrix comparison (analysis)	Matrix derivation (analysis)
Matrix library (element type)	Mature-miRNA - miRBase	Merge binding regions for cell-lines (analysis)
Merge peak callers (analysis)	Merge peaks (analysis)	Merge simulation results (analysis)
Merge table columns (analysis)	Merge track statistics (analysis)	Meta analysis
Metabolic Control Analysis	Metabolic control analysis example	Method (extension point)
Method description HTML file	Methylation probes - Illumina	MiRNA - miRBase
MiRNA feed forward loops (analysis)	MicroRNA aligner (analysis)	MicroRNA finder (analysis)
Microarray (host object)	Mixture of normal components (analysis)	ModelReduction (host object)
Model (host object)	Model analysis	Modeling Antihypertensive drugs
Modeling cardiovascular system	Modular model of the human CVS v.1	Modular model of the human CVS v.2
Modular modeling	Module type (extension point)	Molecular Genetics Library
Motif quality analysis	Moved class (extension point)	Multivariate regression analysis
Multivariate sample analysis	Muscle metabolism	Mutation effect (analysis)
Mutation effect on sites (analysis)	Mutation effect on sites advanced (analysis)	Mutations to genes with weights (analysis)
N-Glycan biosynthesis	NGS misc	Network (host object)
New BioStore	Node (host object)	Non-Linear Mixed Effects Model
Non-merged ChIP-Seq tracks summary (analysis)	Nonlinear Model (analysis)	Normalization quality plots (analysis)
Normalize (host object)	Normalize Affymetrix experiment and control (analysis)	Normalize Agilent experiment and control (analysis)
Normalize Illumina experiment and control (analysis)	Oligonucleotides in sequence samples (analysis)	Open per TF view (analysis)
Open regulated genes table (analysis)	Open tracks for all TF (analysis)	Operations field
Optimization (host object)	Optimization document	Optimization examples
Optimization problem	Orthogonal layout	Outer join (analysis)
Overall circulation model	PASS analysis	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

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