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EBarrays (analysis)	EMBL format	Effector search (analysis)
Element action (extension point)	Element type	Encode quality metrics estimation (analysis)
Enhance Score (analysis)	Enriched upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)	Enrichment (host object)
Enrichment analysis	Ensembl	Ensembl (host object)
Ensembl installation	Ensemble	Enzymes - ExPASy
Enzymes - KEGG	Estimate read density (analysis)	Euler
Evolution strategy (SRES) (analysis)	Explain my genes (workflow)	Export (extension point)
Export element (analysis)	Export master track (analysis)	Export metadata json (analysis)
Export per cell clusters (analysis)	Expression mapping	Extend network (analysis)
Extract RNA length (analysis)	Extract ribosomal RNA (analysis)	Fantom analysis
Fast table filter (analysis)	Fasta format	Fastq compressed (file format)
Fastq format	Fastq mcf	Fastx clip
Features	File (element type)	Filter SPAdes output
Filter duplicate rows (analysis)	Filter one track by another (analysis)	Filter table (analysis)
Filter track by condition (analysis)	Filtering experiments by cell types (analysis)	Filtration of predicted sites by filters (analysis)
Find 10 master regulators in networks (TRANSPATH(R)) (workflow)	Find 3 master regulators in networks with context genes (TRANSPATH(R)) (workflow)	Find common effectors for multiple gene sets (GeneWays) (workflow)
Find common effectors for multiple gene sets (TRANSPATH(R)) (workflow)	Find common effectors in networks (GeneWays) (workflow)	Find common effectors in networks (TRANSPATH(R)) (workflow)
Find enriched TF binding sites in variation sites (TRANSFAC(R)) (workflow)	Find gene fusions from RNA-seq (workflow)	Find genome variants and indels from RNA-seq (workflow)
Find genome variants and indels from full-genome NGS (workflow)	Find longest connected chains (analysis)	Find master regulators for multiple gene sets (GeneWays) (workflow)
Find master regulators for multiple gene sets (TRANSPATH(R)) (workflow)	Find master regulators in mutated network (TRANSPATH(R)) (workflow)	Find master regulators in mutated network (workflow)
Find master regulators in networks (GeneWays) (workflow)	Find master regulators in networks (TRANSPATH(R)) (workflow)	Find master regulators in networks with context genes (TRANSPATH(R)) (workflow)
Find miRNA feed forward loops with CMA (analysis)	Find regulatory regions (analysis)	Find regulatory regions with mutations (analysis)
Find shortest path between two sets (analysis)	Find target genes (analysis)	Find unmappable regions (analysis)
FinderArticlePoints (analysis)	Flux Balance Analysis (workflow)	Flux Balance Constraint (analysis)
Flux balance analysis	Focused upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow)	Fold-Change calculation (analysis)
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

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