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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	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

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