Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
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=== Analysis methods === | === Analysis methods === | ||
Analysis methods defined in this plugin: | Analysis methods defined in this plugin: | ||
| − | *[[Analysis of Binding Regions (analysis)|Analysis of Binding Regions]] | + | *[[File:BSA-Analysis-of-Binding-Regions-icon.png]] [[Analysis of Binding Regions (analysis)|Analysis of Binding Regions]] |
| − | *[[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]] | + | *[[File:BSA-Analysis-of-Cis-Regulatory-Modules-icon.png]] [[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]] |
| − | *[[Analysis of SNPs and Binding sites (analysis)|Analysis of SNPs and Binding sites]] | + | *[[File:BSA-Analysis-of-SNPs-and-Binding-sites-icon.png]] [[Analysis of SNPs and Binding sites (analysis)|Analysis of SNPs and Binding sites]] |
| − | *[[Analysis of five site models (analysis)|Analysis of five site models]] | + | *[[File:BSA-Analysis-of-five-site-models-icon.png]] [[Analysis of five site models (analysis)|Analysis of five site models]] |
| − | *[[Binding regions summary (analysis)|Binding regions summary]] | + | *[[File:Binding-regions-Binding-regions-summary-icon.png]] [[Binding regions summary (analysis)|Binding regions summary]] |
| − | *[[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]] | + | *[[File:BSA-ChIP-seq-peak-profile-icon.png]] [[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]] |
| − | *[[Change profile cutoffs (analysis)|Change profile cutoffs]] | + | *[[File:BSA-Change-profile-cutoffs-icon.png]] [[Change profile cutoffs (analysis)|Change profile cutoffs]] |
| − | *[[Chromosome enrichment (analysis)|Chromosome enrichment]] | + | *[[File:BSA-Chromosome-enrichment-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]] |
| − | *[[Cis-module identification (analysis)|Cis-module identification]] | + | *[[File:Binding-regions-Cis-module-identification-icon.png]] [[Cis-module identification (analysis)|Cis-module identification]] |
| − | *[[Compare site models (analysis)|Compare site models]] | + | *[[File:BSA-Compare-site-models-icon.png]] [[Compare site models (analysis)|Compare site models]] |
| − | *[[Construct IPS CisModule (analysis)|Construct IPS CisModule]] | + | *[[File:BSA-Construct-IPS-CisModule-icon.png]] [[Construct IPS CisModule (analysis)|Construct IPS CisModule]] |
| − | *[[Convert site models to proteins (analysis)|Convert site models to proteins]] | + | *[[File:BSA-Convert-site-models-to-proteins-icon.png]] [[Convert site models to proteins (analysis)|Convert site models to proteins]] |
| − | *[[Convert table to track (analysis)|Convert table to track]] | + | *[[File:BSA-Convert-table-to-track-icon.png]] [[Convert table to track (analysis)|Convert table to track]] |
| − | *[[Count olig frequencies (analysis)|Count olig frequencies]] | + | *[[File:Binding-regions-Count-olig-frequencies-icon.png]] [[Count olig frequencies (analysis)|Count olig frequencies]] |
| − | *[[Create IPS model (analysis)|Create IPS model]] | + | *[[File:BSA-Create-IPS-model-icon.png]] [[Create IPS model (analysis)|Create IPS model]] |
| − | *[[Create Match model (analysis)|Create Match model]] | + | *[[File:BSA-Create-Match-model-icon.png]] [[Create Match model (analysis)|Create Match model]] |
| − | *[[Create matrix by mixture of normal components (analysis)|Create matrix by mixture of normal components]] | + | *[[File:Binding-regions-Create-matrix-by-mixture-of-normal-components-icon.png]] [[Create matrix by mixture of normal components (analysis)|Create matrix by mixture of normal components]] |
| − | *[[Create profile from gene table (analysis)|Create profile from gene table]] | + | *[[File:BSA-Create-profile-from-gene-table-icon.png]] [[Create profile from gene table (analysis)|Create profile from gene table]] |
| − | *[[Create profile from table (analysis)|Create profile from table]] | + | *[[File:BSA-Create-profile-from-table-icon.png]] [[Create profile from table (analysis)|Create profile from table]] |
| − | *[[Create weight matrix model (analysis)|Create weight matrix model]] | + | *[[File:BSA-Create-weight-matrix-model-icon.png]] [[Create weight matrix model (analysis)|Create weight matrix model]] |
| − | *[[Filter one track by another (analysis)|Filter one track by another]] | + | *[[File:BSA-Filter-one-track-by-another-icon.png]] [[Filter one track by another (analysis)|Filter one track by another]] |
| − | *[[Filter track by condition (analysis)|Filter track by condition]] | + | *[[File:BSA-Filter-track-by-condition-icon.png]] [[Filter track by condition (analysis)|Filter track by condition]] |
| − | *[[GC island finder (analysis)|GC island finder]] | + | *[[File:BSA-GC-island-finder-icon.png]] [[GC island finder (analysis)|GC island finder]] |
| − | *[[Gathering genome statistics (analysis)|Gathering genome statistics]] | + | *[[File:Binding-regions-Gathering-genome-statistics-icon.png]] [[Gathering genome statistics (analysis)|Gathering genome statistics]] |
| − | *[[Gene set to track (analysis)|Gene set to track]] | + | *[[File:BSA-Gene-set-to-track-icon.png]] [[Gene set to track (analysis)|Gene set to track]] |
| − | *[[Genome coverage (analysis)|Genome coverage]] | + | *[[File:BSA-Genome-coverage-icon.png]] [[Genome coverage (analysis)|Genome coverage]] |
| − | *[[Heterozygous site caller (analysis)|Heterozygous site caller]] | + | *[[File:BSA-Heterozygous-site-caller-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]] |
| − | *[[IPS motif discovery (analysis)|IPS motif discovery]] | + | *[[File:BSA-IPS-motif-discovery-icon.png]] [[IPS motif discovery (analysis)|IPS motif discovery]] |
| − | *[[Join tracks (analysis)|Join tracks]] | + | *[[File:BSA-Join-tracks-icon.png]] [[Join tracks (analysis)|Join tracks]] |
| − | *[[Merge binding regions for cell-lines (analysis)|Merge binding regions for cell-lines]] | + | *[[File:Binding-regions-Merge-binding-regions-for-cell-lines-icon.png]] [[Merge binding regions for cell-lines (analysis)|Merge binding regions for cell-lines]] |
| − | *[[Merge track statistics (analysis)|Merge track statistics]] | + | *[[File:BSA-Merge-track-statistics-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]] |
| − | *[[MicroRNA aligner (analysis)|MicroRNA aligner]] | + | *[[File:BSA-MicroRNA-aligner-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]] |
| − | *[[Mixture of normal components (analysis)|Mixture of normal components]] | + | *[[File:Binding-regions-Mixture-of-normal-components-icon.png]] [[Mixture of normal components (analysis)|Mixture of normal components]] |
| − | *[[Motif quality analysis]] | + | *[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] |
| − | *[[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] | + | *[[File:Binding-regions-Non-merged-ChIP-Seq-tracks-summary-icon.png]] [[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] |
| − | *[[Preprocess raw reads (analysis)|Preprocess raw reads]] | + | *[[File:BSA-Preprocess-raw-reads-icon.png]] [[Preprocess raw reads (analysis)|Preprocess raw reads]] |
| − | *[[Process track with sites (analysis)|Process track with sites]] | + | *[[File:BSA-Process-track-with-sites-icon.png]] [[Process track with sites (analysis)|Process track with sites]] |
| − | *[[Read counter (analysis)|Read counter]] | + | *[[File:BSA-Read-counter-icon.png]] [[Read counter (analysis)|Read counter]] |
| − | *[[Run MACS 1.3.7 on ChiP-Seq (analysis)|Run MACS 1_3_7 on ChiP-Seq]] | + | *[[File:BSA-Run-MACS-1.3.7-on-ChiP-Seq-icon.png]] [[Run MACS 1.3.7 on ChiP-Seq (analysis)|Run MACS 1_3_7 on ChiP-Seq]] |
| − | *[[Run MACS 1.4.0 on ChiP-Seq (analysis)|Run MACS 1_4_0 on ChiP-Seq]] | + | *[[File:BSA-Run-MACS-1.4.0-on-ChiP-Seq-icon.png]] [[Run MACS 1.4.0 on ChiP-Seq (analysis)|Run MACS 1_4_0 on ChiP-Seq]] |
| − | *[[SNP matching (analysis)|SNP matching]] | + | *[[File:BSA-SNP-matching-icon.png]] [[SNP matching (analysis)|SNP matching]] |
| − | *[[Site counts in repeats (analysis)|Site counts in repeats]] | + | *[[File:BSA-Site-counts-in-repeats-icon.png]] [[Site counts in repeats (analysis)|Site counts in repeats]] |
| − | *[[Site search on gene set (analysis)|Site search on gene set]] | + | *[[File:BSA-Site-search-on-gene-set-icon.png]] [[Site search on gene set (analysis)|Site search on gene set]] |
| − | *[[Site search on track (analysis)|Site search on track]] | + | *[[File:BSA-Site-search-on-track-icon.png]] [[Site search on track (analysis)|Site search on track]] |
| − | *[[Site search result optimization (analysis)|Site search result optimization]] | + | *[[File:BSA-Site-search-result-optimization-icon.png]] [[Site search result optimization (analysis)|Site search result optimization]] |
| − | *[[Site search summary (analysis)|Site search summary]] | + | *[[File:BSA-Site-search-summary-icon.png]] [[Site search summary (analysis)|Site search summary]] |
| − | *[[Track coverage (analysis)|Track coverage]] | + | *[[File:BSA-Track-coverage-icon.png]] [[Track coverage (analysis)|Track coverage]] |
| − | *[[Track statistics (analysis)|Track statistics]] | + | *[[File:BSA-Track-statistics-icon.png]] [[Track statistics (analysis)|Track statistics]] |
=== Importers === | === Importers === | ||
| Line 87: | Line 87: | ||
=== Reference types === | === Reference types === | ||
[[Reference type]]s defined in this plugin: | [[Reference type]]s defined in this plugin: | ||
| − | |||
*[[File:ReferenceType-MatrixTableType-icon.png]] [[Matrices (reference type)|Matrices]] | *[[File:ReferenceType-MatrixTableType-icon.png]] [[Matrices (reference type)|Matrices]] | ||
*[[File:ReferenceType-TransfacMatrixTableType-icon.png]] [[Matrices - TRANSFAC|Matrices: TRANSFAC]] | *[[File:ReferenceType-TransfacMatrixTableType-icon.png]] [[Matrices - TRANSFAC|Matrices: TRANSFAC]] | ||
*[[File:ReferenceType-TransfacProteinType-icon.png]] [[Proteins - Transfac|Proteins: Transfac]] | *[[File:ReferenceType-TransfacProteinType-icon.png]] [[Proteins - Transfac|Proteins: Transfac]] | ||
| + | *[[File:ReferenceType-SNPTableType-icon.png]] [[SNP (reference type)|SNP]] | ||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:ISB plugins]] | [[Category:ISB plugins]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Revision as of 10:34, 10 June 2013
- ID
- ru.biosoft.bsa
- Name
- Bio-sequences analyses plugin
- Provider
- Institute of Systems Biology
- Version
- 0.9.4
Contents |
Analysis methods
Analysis methods defined in this plugin:
- File:BSA-Analysis-of-Binding-Regions-icon.png Analysis of Binding Regions
- 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
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
Create profile from gene table
Create profile from table
Create weight matrix model
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
IPS motif discovery
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:
Reference types
Reference types defined in this plugin:
