Category:ISB analyses

C

• Compare Experiments (analysis)
• Compare site models (analysis)
• Compare TFBS mutations (analysis)
• Compute coverage by window (analysis)
• Compute coverage profile (analysis)
• Compute profile thresholds (analysis)
• ComputeProfileSums (analysis)
• ComputeTranscriptProfile (analysis)
• Construct IPS CisModule (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 miRNA promoters (analysis)
• Create per TF flat files (analysis)
• Create profile from gene table (analysis)
• Create profile from site model table (analysis)
• Create state (analysis)
• Create weight matrix model (analysis)
• CRISPR Cas9 and specific oligonucleotides (analysis)

D

• Data matrix operations (analysis)
• Diagram graph compare 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

• Encode quality metrics estimation (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
• Filter duplicate rows (analysis)
• Filter one track by another (analysis)
• Filter table (analysis)

F cont.

• Filter track by condition (analysis)
• Filtering experiments by cell types (analysis)
• Filtration of predicted sites by filters (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 Table From JSON (analysis)
• Genome coverage (analysis)
• Get transcripts track (analysis)
• GLBSOLVE (analysis)
• Group table rows (analysis)
• GTEX Mutation effect on sites (analysis)
• GTRD analysis
• GTRD analysis advanced (analysis)

H

• 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 HOCOMOCO (analysis)
• Install ExPASy (analysis)
• Install Reactome (analysis)
• IPS motif discovery (analysis)
• IPS prediction (analysis)
• IPS ROC-curves (analysis)
• IPS-scores in SNPs (analysis)
• Isoform TE (analysis)

J

• Join diagrams (analysis)
• Join GTRD clusters (analysis)
• Join GTRD Tracks (analysis)
• Join several tables (analysis)
• Join table (analysis)
• Join tracks (analysis)
• Join two tables (analysis)

K

• Key Node Sensitivity Analysis

L

• Large sequence minimal unique length (analysis)
• LincRNA and mRNA features (analysis)
• Linear Shifted Model (analysis)
• Locations of best sites (analysis)
• LS-regression analysis

M

• Make GTF for riboseq alignment (analysis)
• Make meta tracks (analysis)
• Mappability histogram (analysis)
• Mass Conservation Analysis
• Match genes and metabolites (analysis)
• Matrix comparison (analysis)
• Matrix derivation (analysis)
• 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

M cont.

• MicroRNA aligner (analysis)
• MicroRNA finder (analysis)
• Mixture of normal components (analysis)
• Model analysis
• Motif quality analysis
• Multivariate regression analysis
• Multivariate sample analysis
• Mutation effect (analysis)
• Mutation effect on sites (analysis)
• Mutation effect on sites advanced (analysis)

N

• Non-merged ChIP-Seq tracks summary (analysis)
• Nonlinear Model (analysis)

O

• Oligonucleotides in sequence samples (analysis)
• Open per TF view (analysis)
• Open regulated genes table (analysis)
• Open tracks for all TF (analysis)

P

• Parameter fitting (analysis)
• Parameter identifiability (optimization) (analysis)
• Parameter identifiability (table) (analysis)
• Particle swarm optimization (analysis)
• PASS analysis
• Peak finders comparison (analysis)
• Plot bar chart (analysis)
• Plot pie chart (analysis)
• Plot scatter chart (analysis)
• Plot2D (analysis)
• Polynomial Regression analysis
• Population generation (analysis)
• Prediction of TF-binding sites of given TF (analysis)
• PredictStartSites (analysis)
• Prepare cluster to exp table (analysis)
• Prepare finished tables (analysis)
• Prepare GTF annotation (analysis)
• Prepare Search by regulation (analysis)
• Prepare target genes by expression (analysis)
• Preprocess raw reads (analysis)
• Process track with sites (analysis)
• Profiles Statistics (analysis)

Q

• Quadratic Hill-climbing (analysis)
• Quality control analysis
• Quality control metrics (analysis)
• Quantile normalization (analysis)
• Quasi-Steady-State Analysis

R

• Reactions Analysis
• Read counter (analysis)
• Rebuild search indexes (analysis)
• Recon transformer (analysis)
• Reduce track (analysis)
• Regression analysis
• Regression analysis advanced (analysis)
• Remove overlapping sites (analysis)
• Remove unobservable molecules (analysis)
• Report (analysis)
• Report generator for quality control analysis
• Ribo-Seq and mRNA features forming (analysis)
• RiboseqArticleResult (analysis)
• RiboSeqExp (analysis)
• RNA-Seq analysis
• ROC curves for best sites union (analysis)
• ROC-curves in clusterized peaks (analysis)
• ROC-curves in grouped peaks (analysis)
• ROC-curves in overlapped ChIP-Seq peaks (analysis)
• Run a Workflow as Analysis
• Run analysis
• Run MACS 1.3.7 on ChiP-Seq (analysis)
• Run MACS 1.4.0 on ChiP-Seq (analysis)