Category:Autogenerated pages

A

• Admin (analyses group)
• Autosome.Ru analyses
• Autosome.Ru plugins
• Autosome.Ru workflows

B

• Binding regions (analyses group)
• Biosoft analyses
• Biosoft plugins
• BSA (analyses group)

C

• ChIP-seq (analyses group)
• ChIPMunk (analyses group)
• Colon cancer signature (analyses group)
• Composite module analyses (analyses group)
• Creasemarks (analyses group)

D

• DAE models (analyses group)
• DAS (analyses group)
• Data (analyses group)
• DevelopmentOnTheEdge.com plugins
• Differential algebraic equations (analyses group)

G

• Gene models (analyses group)
• Gene set analysis (analyses group)

G cont.

• GeneModels (analyses group)
• GeneXplain analyses
• GeneXplain plugins
• GeneXplain workflows
• Genome enhancer (analyses group)
• GTEX (analyses group)
• GTRD (analyses group)
• GTRD build (analyses group)

I

• Import (analyses group)
• ISB analyses
• ISB plugins

M

• Machine learning (analyses group)
• Match sites and genes (analyses group)
• Microarray normalization (analyses group)
• MicroRNA (analyses group)
• MiRNA (analyses group)
• Molecular networks (analyses group)
• Motif discovery (analyses group)
• Mutations (analyses group)

N

• NGS color-space (analyses group)

N cont.

• NGS utils (analyses group)

O

• Operations with genomic tracks (analyses group)
• Optimization (analyses group)

P

• Parameter fitting (analyses group)
• Plots and charts (analyses group)
• Population (analyses group)

R

• RiboSeq (analyses group)
• RiboseqArticleResult (analyses group)
• Ribosome profiling (analyses group)
• RNA-seq (analyses group)

S

• SEDML (analyses group)
• Sequence mappability (analyses group)
• Simulation (analyses group)
• Softberry plugins
• Statistics (analyses group)

T

• Table manipulation (analyses group)
• TF binding site search (analyses group)
• Trash (analyses group)

U

• Unclassified (analyses group)

W

• Workflow utils (analyses group)

A

• Adaptive simulated annealing (analysis)
• Add calculated column (analysis)
• Add expression values (analysis)
• Add genes from CMA (analysis)
• Add reactants (analysis)
• Affymetrix CEL file
• Affymetrix normalization (analysis)
• Agilent microarray file
• Agilent normalization (analysis)
• Algebraic steady state (analysis)
• Analysis of Binding Regions (analysis)
• Analysis of Cis-Regulatory Modules (analysis)
• Analyze any DNA sequence (GTRD) (workflow)
• Analyze any DNA sequence (TRANSFAC(R)) (workflow)
• Analyze any DNA sequence for site enrichment (GTRD) (workflow)
• Analyze any DNA sequence for site enrichment (TRANSFAC(R)) (workflow)
• Analyze any DNA sequence, EMBL (workflow)
• Analyze any DNA sequence, Fasta (workflow)
• Analyze any DNA sequence, GeneBank (workflow)
• Analyze miRNA target enrichment (analysis)
• Analyze promoters (GTRD) (workflow)
• Analyze promoters (TRANSFAC(R)) (workflow)
• Analyze SNP list (GTRD) (workflow)
• Analyze SNP list (TRANSFAC(R)) (workflow)
• Annotate diagram (analysis)
• Annotate table (analysis)
• Annotate track with genes (analysis)
• Antimony (file format)
• Apply CMA model to tracks (analysis)
• Apply events (analysis)
• Apply state to diagram (analysis)
• ArticleComparator (analysis)
• ArticleTrackCreator (analysis)
• AUC Estimation For meta-cluster track (analysis)

B

• BAM filter multi-hits (analysis)
• BAM filter strand specific (analysis)
• BED format
• Binding regions summary (analysis)
• Biohub (host object)
• BioNetGen language format
• BioPAX file
• BioUML format
• BioUML Simulation result (file format)
• Biouml.plugins.affymetrix (plugin)
• Biouml.plugins.agentmodeling (plugin)
• Biouml.plugins.agilent (plugin)
• Biouml.plugins.antimony (plugin)
• Biouml.plugins.bindingregions (plugin)
• Biouml.plugins.bionetgen (plugin)
• Biouml.plugins.biopax (plugin)
• Biouml.plugins.bkl (plugin)
• Biouml.plugins.bowtie (plugin)
• Biouml.plugins.ccsignature (plugin)
• Biouml.plugins.cellml (plugin)
• Biouml.plugins.chebi (plugin)
• Biouml.plugins.chemoinformatics (plugin)
• Biouml.plugins.chipmunk (plugin)
• Biouml.plugins.cma (plugin)
• Biouml.plugins.creasemarks (plugin)
• Biouml.plugins.cytoscape (plugin)
• Biouml.plugins.das (plugin)
• Biouml.plugins.download (plugin)
• Biouml.plugins.dropbox (plugin)
• Biouml.plugins.endonet (plugin)
• Biouml.plugins.enrichment (plugin)
• Biouml.plugins.ensembl (plugin)
• Biouml.plugins.expasy (plugin)

B cont.

• Biouml.plugins.expression (plugin)
• Biouml.plugins.fbc (plugin)
• Biouml.plugins.genemodels (plugin)
• Biouml.plugins.genenet (plugin)
• Biouml.plugins.geneways (plugin)
• Biouml.plugins.genomeenhancer (plugin)
• Biouml.plugins.ginsim (plugin)
• Biouml.plugins.glycan (plugin)
• Biouml.plugins.gne (plugin)
• Biouml.plugins.go (plugin)
• Biouml.plugins.googledrive (plugin)
• Biouml.plugins.graphml (plugin)
• Biouml.plugins.gtrd (plugin)
• Biouml.plugins.gxl (plugin)
• Biouml.plugins.hemodynamics (plugin)
• Biouml.plugins.illumina (plugin)
• Biouml.plugins.kegg (plugin)
• Biouml.plugins.keynodes (plugin)
• Biouml.plugins.lucene (plugin)
• Biouml.plugins.machinelearning (plugin)
• Biouml.plugins.matlab (plugin)
• Biouml.plugins.metabolics (plugin)
• Biouml.plugins.microarray (plugin)
• Biouml.plugins.mirbase (plugin)
• Biouml.plugins.miriam (plugin)
• Biouml.plugins.mirprom (plugin)
• Biouml.plugins.modelreduction (plugin)
• Biouml.plugins.node (plugin)
• Biouml.plugins.obo (plugin)
• Biouml.plugins.optimization (plugin)
• Biouml.plugins.pass (plugin)
• Biouml.plugins.pathfinder (plugin)
• Biouml.plugins.perfectosape (plugin)
• Biouml.plugins.pharm (plugin)
• Biouml.plugins.proteinmodel (plugin)
• Biouml.plugins.psimi (plugin)
• Biouml.plugins.reactome (plugin)
• Biouml.plugins.reactome.biohub (plugin)
• Biouml.plugins.research (plugin)
• Biouml.plugins.riboseq (plugin)
• Biouml.plugins.riboseqArticleResult (plugin)
• Biouml.plugins.sabiork (plugin)
• Biouml.plugins.sbgn (plugin)
• Biouml.plugins.sbml (plugin)
• Biouml.plugins.sbw (plugin)
• Biouml.plugins.sedml (plugin)
• Biouml.plugins.seek (plugin)
• Biouml.plugins.server (plugin)
• Biouml.plugins.simulation (plugin)
• Biouml.plugins.simulation-test (plugin)
• Biouml.plugins.softberry (plugin)
• Biouml.plugins.stochastic (plugin)
• Biouml.plugins.svg (plugin)
• Biouml.plugins.test (plugin)
• Biouml.plugins.transfac (plugin)
• Biouml.plugins.transpath (plugin)
• Biouml.plugins.uniprot (plugin)
• Biouml.plugins.users (plugin)
• Biouml.plugins.wiki (plugin)
• Biouml.workbench (plugin)
• Biouml.workbench.graph (plugin)
• Blast alignment coverage (analysis)
• Bowtie (analysis)
• Breakdancer output (file format)
• Bsa (host object)
• BuildASiteOffsetTable (analysis)
• Building Flux Balance DataTable (analysis)

B cont.

• BuildProfileModel (analysis)

C

• Calculate CMA regulation (analysis)
• Calculate keynodes ranks (analysis)
• Calculate TFs regulatory score (analysis)
• Calculate weighted mutation score (analysis)
• Categories (reference type)
• Categories - BKL
• Categories - ExPASy
• Categories - Gene ontology
• Categories - GTRD
• Cdk (host object)
• Cell - EndoNet
• CellML (file format)
• Cellular genetic algorithm (analysis)
• Change diagram (analysis)
• Change profile cutoffs (analysis)
• Check quotas (analysis)
• Check Workflow consistency (analysis)
• ChIP experiment - GTRD
• 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 - 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 characteristics distribution (analysis)
• ChIP-seq peak profile (analysis)
• ChIP-seq peaks - GTRD
• ChIP-Seq peaks clusterization (analysis)
• ChIP-seq Quality control analysis
• ChIPHorde (analysis)
• ChIPMunk (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)
• Clean up SQL database (analysis)
• Cluster analysis
• Cluster analysis by K-means (analysis)
• Cluster by path (analysis)
• Cluster by shortest path (analysis)
• Cluster track (analysis)
• CMA Result Statistic (analysis)
• CNVnator genotype output (file format)
• Colon cancer signature (analysis)
• Colon cancer signature2 (analysis)
• Color space to nucleotide (analysis)
• Com.developmentontheedge.beans (plugin)
• Com.developmentontheedge.server (plugin)
• Com.developmentontheedge.util (plugin)
• Common and IPS scores correlation (analysis)
• Compare analysis results (analysis)
• Compare Experiments (analysis)
• Compare site models (analysis)
• Compare TFBS mutations (analysis)
• Composite module to proteins (analysis)
• Compute coverage by window (analysis)
• Compute coverage profile (analysis)
• Compute differentially expressed genes (Affymetrix probes) (workflow)
• Compute differentially expressed genes (Agilent probes) (workflow)
• Compute differentially expressed genes (Agilent Tox probes) (workflow)
• Compute differentially expressed genes (Illumina probes) (workflow)