Difference between revisions of "Ru.biosoft.bsa (plugin)"
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=== Analysis methods === | === Analysis methods === | ||
Analysis methods defined in this plugin: | Analysis methods defined in this plugin: | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Analysis of SNPs and Binding sites (analysis)|Analysis of SNPs and Binding sites]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Analysis of five site models (analysis)|Analysis of five site models]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Binding regions summary (analysis)|Binding regions summary]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[ChIP-Seq characteristics distribution (analysis)|ChIP-Seq characteristics distribution]] |
*[[File:BSA-ChIP-seq-peak-profile-icon.png]] [[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]] | ||
*[[File:BSA-Change-profile-cutoffs-icon.png]] [[Change profile cutoffs (analysis)|Change profile cutoffs]] | *[[File:BSA-Change-profile-cutoffs-icon.png]] [[Change profile cutoffs (analysis)|Change profile cutoffs]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Cis-module identification (analysis)|Cis-module identification]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Compare site models (analysis)|Compare site models]] |
*[[File:BSA-Construct-IPS-CisModule-icon.png]] [[Construct IPS CisModule (analysis)|Construct IPS CisModule]] | *[[File:BSA-Construct-IPS-CisModule-icon.png]] [[Construct IPS CisModule (analysis)|Construct IPS CisModule]] | ||
*[[File:BSA-Convert-site-models-to-proteins-icon.png]] [[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]] | ||
*[[File:BSA-Convert-table-to-track-icon.png]] [[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]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Count olig frequencies (analysis)|Count olig frequencies]] |
*[[File:BSA-Create-IPS-model-icon.png]] [[Create IPS model (analysis)|Create IPS model]] | *[[File:BSA-Create-IPS-model-icon.png]] [[Create IPS model (analysis)|Create IPS model]] | ||
*[[File:BSA-Create-Match-model-icon.png]] [[Create Match model (analysis)|Create Match model]] | *[[File:BSA-Create-Match-model-icon.png]] [[Create Match model (analysis)|Create Match model]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Create matrix by mixture of normal components (analysis)|Create matrix by mixture of normal components]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Create matrix by mixture of normal components (ChIP-seq) (analysis)|Create matrix by mixture of normal components (ChIP-seq)]] |
*[[File:BSA-Create-profile-from-gene-table-icon.png]] [[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]] | ||
*[[File:BSA-Create-profile-from-table-icon.png]] [[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]] | ||
*[[File:BSA-Create-weight-matrix-model-icon.png]] [[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]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Distinct TF classes (analysis)|Distinct TF classes]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]] |
*[[File:BSA-Filter-one-track-by-another-icon.png]] [[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]] | ||
*[[File:BSA-Filter-track-by-condition-icon.png]] [[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]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[GC island finder (analysis)|GC island finder]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Gathering genome statistics (analysis)|Gathering genome statistics]] |
*[[File:BSA-Gene-set-to-track-icon.png]] [[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]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Genome coverage (analysis)|Genome coverage]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[IPS ROC-curves (analysis)|IPS ROC-curves]] |
*[[File:BSA-IPS-motif-discovery-icon.png]] [[IPS motif discovery (analysis)|IPS motif discovery]] | *[[File:BSA-IPS-motif-discovery-icon.png]] [[IPS motif discovery (analysis)|IPS motif discovery]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[IPS prediction (analysis)|IPS prediction]] |
*[[File:BSA-Join-tracks-icon.png]] [[Join tracks (analysis)|Join tracks]] | *[[File:BSA-Join-tracks-icon.png]] [[Join tracks (analysis)|Join tracks]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Merge binding regions for cell-lines (analysis)|Merge binding regions for cell-lines]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Mixture of normal components (analysis)|Mixture of normal components]] |
*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | *[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Preprocess raw reads (analysis)|Preprocess raw reads]] |
*[[File:BSA-Process-track-with-sites-icon.png]] [[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]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Read counter (analysis)|Read counter]] |
*[[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]] | *[[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]] | ||
*[[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]] | *[[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]] | ||
*[[File:BSA-SNP-matching-icon.png]] [[SNP matching (analysis)|SNP matching]] | *[[File:BSA-SNP-matching-icon.png]] [[SNP matching (analysis)|SNP matching]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Site counts in repeats (analysis)|Site counts in repeats]] |
*[[File:BSA-Site-search-on-gene-set-icon.png]] [[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]] | ||
*[[File:BSA-Site-search-on-track-icon.png]] [[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]] | ||
*[[File:BSA-Site-search-result-optimization-icon.png]] [[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]] | ||
*[[File:BSA-Site-search-summary-icon.png]] [[Site search summary (analysis)|Site search summary]] | *[[File:BSA-Site-search-summary-icon.png]] [[Site search summary (analysis)|Site search summary]] | ||
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]] |
| − | *[[File: | + | *[[File:Default-analysis-icon.png]] [[Track statistics (analysis)|Track statistics]] |
=== Importers === | === Importers === | ||
Revision as of 18:09, 14 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:
Analysis of Cis-Regulatory Modules
- Analysis of SNPs and Binding sites
- Analysis of five site models
- Binding regions summary
- ChIP-Seq characteristics distribution
ChIP-seq peak profile
Change profile cutoffs
- Chromosome enrichment
- Cis-module identification
- Compare site models
Construct IPS CisModule
Convert site models to proteins
Convert table to track
- Count olig frequencies
Create IPS model
Create Match model
- Create matrix by mixture of normal components
- Create matrix by mixture of normal components (ChIP-seq)
Create profile from gene table
Create profile from table
Create weight matrix model
- Distinct TF classes
- Extract ribosomal RNA
Filter one track by another
Filter track by condition
- GC island finder
- Gathering genome statistics
Gene set to track
- Genome coverage
- Heterozygous site caller
- IPS ROC-curves
IPS motif discovery
- IPS prediction
Join tracks
- Merge binding regions for cell-lines
- Merge track statistics
- MicroRNA aligner
- Mixture of normal components
Motif quality analysis
- 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
- Site counts in repeats
Site search on gene set
Site search on track
Site search result optimization
Site search summary
- 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:
