Category:Analyses

A

• Admin (analyses group)
• Autosome.Ru analyses

B

• Binding regions (analyses group)
• Biosoft analyses
• 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)
• Differential algebraic equations (analyses group)

G

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

G cont.

• Genome enhancer (analyses group)
• GTEX (analyses group)
• GTRD (analyses group)
• GTRD build (analyses group)

I

• Import (analyses group)
• ISB analyses

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)
• 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)
• 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 normalization (analysis)
• Agilent normalization (analysis)
• Algebraic steady state (analysis)
• Analysis of Binding Regions (analysis)
• Analysis of Cis-Regulatory Modules (analysis)
• Analyze miRNA target enrichment (analysis)
• Annotate diagram (analysis)
• Annotate table (analysis)
• Annotate track with genes (analysis)
• 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)
• Binding regions summary (analysis)
• Blast alignment coverage (analysis)
• Bowtie (analysis)
• BuildASiteOffsetTable (analysis)
• Building Flux Balance DataTable (analysis)
• BuildProfileModel (analysis)

C

• Calculate CMA regulation (analysis)
• Calculate keynodes ranks (analysis)
• Calculate TFs regulatory score (analysis)
• Calculate weighted mutation score (analysis)
• Cellular genetic algorithm (analysis)
• Change diagram (analysis)
• Change profile cutoffs (analysis)
• Check quotas (analysis)
• Check Workflow consistency (analysis)
• ChIP-Seq characteristics distribution (analysis)
• ChIP-seq peak profile (analysis)
• ChIP-Seq peaks clusterization (analysis)
• ChIP-seq Quality control analysis
• ChIPHorde (analysis)
• ChIPMunk (analysis)
• 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)
• Colon cancer signature (analysis)
• Colon cancer signature2 (analysis)
• Color space to nucleotide (analysis)
• 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)

C cont.

• Compute coverage profile (analysis)
• Compute profile thresholds (analysis)
• ComputeProfileSums (analysis)
• ComputeTranscriptProfile (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)
• Construct IPS CisModule (analysis)
• Continue CMA (analysis)
• Convert diagram to pairs (analysis)
• Convert diagram to Transpath (analysis)
• Convert files to tracks (analysis)
• Convert genomic BAM to transcriptomic (analysis)
• Convert site models to proteins (analysis)
• Convert site search summary (analysis)
• Convert table (analysis)
• Convert table to track (analysis)
• Convert table to VCF track (analysis)
• Convert table via homology (analysis)
• Convert tracks to VCF (analysis)
• Copy data element (analysis)
• Copy folder (analysis)
• Correlation Analysis
• Correlations of best sites (analysis)
• Count olig frequencies (analysis)
• Count reads in transcripts (analysis)
• Coverage Profiles Cutoff (analysis)
• CoverageCheker (analysis)
• CR cluster selector (analysis)
• CRC Analysis
• Creasemarks analysis
• Create custom project (analysis)
• Create DAS track (analysis)
• Create database from diagram (analysis)
• Create flat files (analysis)
• Create folder (analysis)
• Create IPS model (analysis)
• Create Match model (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)
• CRISPR Cas9 and specific oligonucleotides (analysis)

D

• Data matrix operations (analysis)
• Diagram graph compare analysis
• Diagram to user hub collection (analysis)
• DiChIPHorde (analysis)
• DiChIPMunk (analysis)
• Differential expression with DESeq (analysis)
• Distinct TF classes (analysis)
• DNase-seq Group and Profile Generation (analysis)
• DNase-seq Group and Profile Generation (Previous version) (analysis)
• Double encode SOLiD (analysis)
• Download model (analysis)

E

• EBarrays (analysis)

E cont.

• Effector search (analysis)
• Encode quality metrics estimation (analysis)
• Enhance Score (analysis)
• Enrichment analysis
• Estimate read density (analysis)
• Evolution strategy (SRES) (analysis)
• Export element (analysis)
• Export master track (analysis)
• Export metadata json (analysis)
• Export per cell clusters (analysis)
• Extend network (analysis)
• Extract ribosomal RNA (analysis)
• Extract RNA length (analysis)

F

• Fantom analysis
• Fast table filter (analysis)
• 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 longest connected chains (analysis)
• 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 Constraint (analysis)
• Fold-Change calculation (analysis)
• Functional classification (analysis)
• Functional classification by diagrams (analysis)

G

• Gathering genome statistics (analysis)
• GC island finder (analysis)
• Gene features (analysis)
• Gene overlap statistics (analysis)
• Gene set to track (analysis)
• Generate dynamic model (analysis)
• Generate Table From JSON (analysis)
• Generate workflow from annotation diagram (analysis)
• Genome coverage (analysis)
• Get miRNA targets (analysis)
• Get transcripts track (analysis)
• GLBSOLVE (analysis)
• GlycanR (analysis)
• Group table rows (analysis)
• GTEX Mutation effect on sites (analysis)
• GTRD analysis
• GTRD analysis advanced (analysis)
• Guided linear model analysis

H

• Heatmap (analysis)
• Heterozygous site caller (analysis)
• Hypergeometric analysis

I

• 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)
• Illumina metylation probes to track (analysis)
• Illumina normalization (analysis)
• Import ensembl homology (analysis)
• Import from BC Platform (analysis)
• Import from TranSMART (analysis)
• Import HOCOMOCO (analysis)
• Infer network (analysis)
• Install ExPASy (analysis)
• Install HumanPSD(TM) database (analysis)