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1-dimensional arterial tree model3D viewerAUC Estimation For meta-cluster track (analysis)
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Analyze any DNA sequence for site enrichment (GTRD) (workflow)Analyze any DNA sequence for site enrichment (TRANSFAC(R)) (workflow)Analyze miRNA target enrichment (analysis)
Analyze promoters (GTRD) (workflow)Analyze promoters (TRANSFAC(R)) (workflow)Annotate diagram (analysis)
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Biouml.workbench (plugin)BioumlsimBlast alignment coverage (analysis)
Bowtie (analysis)Breakdancer output (file format)Bsa (host object)
BuildASiteOffsetTable (analysis)BuildProfileModel (analysis)Building Flux Balance DataTable (analysis)
C-tauCMA Result Statistic (analysis)CNVnator genotype output (file format)
COVID-19 parameters for IntestineCOVID-19 parameters for LungCOVID-19 parameters for Nasopharynx
CRC AnalysisCRISPR Cas9 and specific oligonucleotides (analysis)CR cluster selector (analysis)
CWLCalculate CMA regulation (analysis)Calculate TFs regulatory score (analysis)
Calculate keynodes ranks (analysis)Calculate weighted mutation score (analysis)Categories (reference type)
Categories - BKLCategories - ExPASyCategories - GTRD
Categories - Gene ontologyCdk (host object)CellML (file format)
Cell - EndoNetCell type specific TFBS predictionCellular genetic algorithm (analysis)
ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R)) (workflow)ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R)) (workflow)ChIP-Seq - Identify and classify target genes (HumanPSD(TM)) (workflow)
ChIP-Seq - Identify and classify target genes (TRANSPATH(R)) (workflow)ChIP-Seq - Identify and classify target genes (workflow)ChIP-Seq - Identify composite modules on peaks (TRANSFAC(R)) (workflow)
ChIP-Seq characteristics distribution (analysis)ChIP-Seq peaks clusterization (analysis)ChIP-seq Analysis
ChIP-seq Quality control analysisChIP-seq peak profile (analysis)ChIP-seq peaks - GTRD
ChIPHorde (analysis)ChIPMunk (analysis)ChIPMunk (perspective)
ChIP experiment - GTRDChange diagram (analysis)Change profile cutoffs (analysis)
Check Workflow consistency (analysis)Check quotas (analysis)Chipmunk (host object)
ChromatinInfo table creation (analysis)Chromosome enrichment (analysis)Cis-module identification (analysis)
Cis-module sets near given genes (analysis)Cistrom construction (analysis)Classification analysis
Classification analysis advanced (analysis)Classification hubClean up SQL database (analysis)
CloudBioLinuxCloudManCluster analysis
Cluster analysis by K-means (analysis)Cluster by path (analysis)Cluster by shortest path (analysis)
Cluster track (analysis)Collaborative diagram editingColon cancer signature2 (analysis)
Colon cancer signature (analysis)Color space to nucleotide (analysis)Com.developmentontheedge.beans (plugin)
Com.developmentontheedge.server (plugin)Com.developmentontheedge.util (plugin)Combined track
Common and IPS scores correlation (analysis)Common class (extension point)Compare Experiments (analysis)
Compare TFBS mutations (analysis)Compare analysis results (analysis)Compare site models (analysis)
Composite module to proteins (analysis)ComputeProfileSums (analysis)ComputeTranscriptProfile (analysis)
Compute coverage by window (analysis)Compute coverage profile (analysis)Compute differentially expressed genes (Affymetrix probes) (workflow)
Compute differentially expressed genes (Agilent Tox probes) (workflow)Compute differentially expressed genes (Agilent probes) (workflow)Compute differentially expressed genes (Illumina probes) (workflow)
Compute differentially expressed genes using EBarrays (workflow)Compute differentially expressed genes using Hypergeometric test (Affymetrix probes) (workflow)Compute differentially expressed genes using Hypergeometric test (Agilent probes) (workflow)
Compute differentially expressed genes using Hypergeometric test (Illumina probes) (workflow)Compute differentially expressed genes using Limma (workflow)Compute profile thresholds (analysis)
Construct IPS CisModule (analysis)Construct composite modules (analysis)Construct composite modules on track (correlation) (analysis)
Construct composite modules on tracks (analysis)Construct composite modules on tracks (without site search) (analysis)Construct composite modules on tracks with keynodes (analysis)
Construct composite modules with keynodes (analysis)Context item (extension point)Continue CMA (analysis)
ContributorsConvert diagram to Transpath (analysis)Convert diagram to pairs (analysis)
Convert files to tracks (analysis)Convert genomic BAM to transcriptomic (analysis)Convert identifiers for multiple gene sets (workflow)
Convert site models to proteins (analysis)Convert site search summary (analysis)Convert table (analysis)
Convert table to VCF track (analysis)Convert table to track (analysis)Convert table via homology (analysis)
Convert tracks to VCF (analysis)Copy data element (analysis)Copy folder (analysis)
Correlation AnalysisCorrelations of best sites (analysis)Count olig frequencies (analysis)
Count reads in transcripts (analysis)CoverageCheker (analysis)Coverage Profiles Cutoff (analysis)
Covid-19 Differential Delay ModelCovid 19Covid 19 parameters
Creasemarks analysisCreate DAS track (analysis)Create IPS model (analysis)
Create Match model (analysis)Create custom project (analysis)Create database from diagram (analysis)
Create flat files (analysis)Create folder (analysis)Create matrix by mixture of normal components (analysis)
Create matrix logo (analysis)Create miRNA promoters (analysis)Create per TF flat files (analysis)
Create profile from CMA model (analysis)Create profile from gene table (analysis)Create profile from matrix library (analysis)
Create profile from site model table (analysis)Create random track (analysis)Create state (analysis)
Create tissue-specific promoter track (analysis)Create transcript region track (analysis)Create weight matrix model (analysis)
Creating Galaxy toolCross-species identification of enriched motifs in promoters, using orthologue information (TRANSFAC(R)) (workflow)Cross-species mapping to ontologies, using orthologue information (HumanPSD(TM)) (workflow)
Cross cost grid layoutCytoscape network formatDAE Models examples
DDMoRe consortiumDNase-seq Group and Profile Generation (Previous version) (analysis)DNase-seq Group and Profile Generation (analysis)
Dannon et al. Covid-19 transmission in England
Danon et al. Covid-19 transmission in EnglandDas (host object)
DataFilter (host object)Data (host object)Data collection listener (extension point)
Data matrix operations (analysis)DatabasesDatabases installation
Default (perspective)Defines.jsDescrete events
Developed modelsDiChIPHorde (analysis)DiChIPMunk (analysis)
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