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Diagram (element type)	Diagram document	Diagram editing history
Diagram graph compare analysis	Diagram to user hub collection (analysis)	Diagram type
Diagram view part (extension point)	Diff manager (extension point)	Differential expression with DESeq (analysis)
Disease - MeSH	Distinct TF classes (analysis)	Docker meta
Document factory (extension point)	Document pane	Dormand-Prince
Double encode SOLiD (analysis)	Download	Download model (analysis)
Drugs - DrugBank	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

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