Category:ISB analyses

A

• Adaptive simulated annealing (analysis)
• Add calculated column (analysis)
• Add expression values (analysis)
• Affymetrix normalization (analysis)
• Agilent normalization (analysis)
• Algebraic steady state (analysis)
• Analysis of Binding Regions (analysis)
• Analysis of Cis-Regulatory Modules (analysis)
• Annotate diagram (analysis)
• Annotate table (analysis)
• Annotate track with genes (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

• 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
• 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 track (analysis)
• Colon cancer signature (analysis)
• Colon cancer signature2 (analysis)
• Color space to nucleotide (analysis)
• Common and IPS scores correlation (analysis)
• 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)

C cont.

• 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)
• 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)

G cont.

• 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
• 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)