Ru.biosoft.bsa (plugin)

ID

ru.biosoft.bsa

Name

Bio-sequences analyses plugin

Provider

Institute of Systems Biology

Version

0.9.4

Analysis methods

Analysis methods defined in this plugin:

• File:BSA-Analysis-of-Cis-Regulatory-Modules-icon.png Analysis of Cis-Regulatory Modules
• File:BSA-Analysis-of-SNPs-and-Binding-sites-icon.png Analysis of SNPs and Binding sites
• File:BSA-Analysis-of-five-site-models-icon.png Analysis of five site models
• File:Binding-regions-Binding-regions-summary-icon.png Binding regions summary
• File:Binding-regions-ChIP-Seq-characteristics-distribution-icon.png ChIP-Seq characteristics distribution
• ChIP-seq peak profile
• Change profile cutoffs
• File:BSA-Chromosome-enrichment-icon.png Chromosome enrichment
• File:Binding-regions-Cis-module-identification-icon.png Cis-module identification
• File:BSA-Compare-site-models-icon.png Compare site models
• Construct IPS CisModule
• Convert site models to proteins
• Convert table to track
• File:Binding-regions-Count-olig-frequencies-icon.png Count olig frequencies
• Create IPS model
• Create Match model
• File:Binding-regions-Create-matrix-by-mixture-of-normal-components-icon.png Create matrix by mixture of normal components
• File:Binding-regions-Create-matrix-by-mixture-of-normal-components-(ChIP-seq)-icon.png Create matrix by mixture of normal components (ChIP-seq)
• Create profile from gene table
• Create profile from table
• Create weight matrix model
• File:Binding-regions-Distinct-TF-classes-icon.png Distinct TF classes
• File:BSA-Extract-ribosomal-RNA-icon.png Extract ribosomal RNA
• Filter one track by another
• Filter track by condition
• File:BSA-GC-island-finder-icon.png GC island finder
• File:Binding-regions-Gathering-genome-statistics-icon.png Gathering genome statistics
• Gene set to track
• File:BSA-Genome-coverage-icon.png Genome coverage
• File:BSA-Heterozygous-site-caller-icon.png Heterozygous site caller
• File:Binding-regions-IPS-ROC-curves-icon.png IPS ROC-curves
• IPS motif discovery
• File:Binding-regions-IPS-prediction-icon.png IPS prediction
• Join tracks
• File:Binding-regions-Merge-binding-regions-for-cell-lines-icon.png Merge binding regions for cell-lines
• File:BSA-Merge-track-statistics-icon.png Merge track statistics
• File:BSA-MicroRNA-aligner-icon.png MicroRNA aligner
• File:Binding-regions-Mixture-of-normal-components-icon.png Mixture of normal components
• Motif quality analysis
• File:Binding-regions-Non-merged-ChIP-Seq-tracks-summary-icon.png Non-merged ChIP-Seq tracks summary
• Preprocess raw reads
• Process track with sites
• Read counter
• Run MACS 1_3_7 on ChiP-Seq
• Run MACS 1_4_0 on ChiP-Seq
• SNP matching
• File:BSA-Site-counts-in-repeats-icon.png Site counts in repeats
• Site search on gene set
• Site search on track
• Site search result optimization
• Site search summary
• File:BSA-Track-coverage-icon.png Track coverage
• Track statistics

Importers

Data element importers for the following file formats are defined in this plugin:

• BED format (*.bed)
• Breakdancer output (*.ctx)
• CNVnator genotype output (*.genotype)
• EMBL format (*.embl)
• Fasta format (*.fasta)
• Fastq as track (*.fastq)
• Fastq format (*.fastq)
• GenBank format (*.gb)
• Gene Transfer Format (*.gtf)
• General Feature Format (*.gff)
• Interval format (*.interval)
• Pindel output
• SAM or BAM alignment file (*.sam, *.bam)
• SISSRs output (*.bsites)
• VAT output (*.vat)
• VCF format (*.vcf)
• Varscan output
• Wiggle format (*.wig)

Host objects

JavaScript host objects defined in this plugin:

• bsa
• siteAnalysis

Reference types

Reference types defined in this plugin:

• Matrices
• Matrices: TRANSFAC
• Proteins: Transfac
• SNP