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: | ||
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*[[File:BSA-Analysis-of-Cis-Regulatory-Modules-icon.png]] [[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]] | ||
*[[File:BSA-Analysis-of-SNPs-and-Binding-sites-icon.png]] [[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]] | ||
*[[File:BSA-Analysis-of-five-site-models-icon.png]] [[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]] | ||
*[[File:Binding-regions-Binding-regions-summary-icon.png]] [[Binding regions summary (analysis)|Binding regions summary]] | *[[File:Binding-regions-Binding-regions-summary-icon.png]] [[Binding regions summary (analysis)|Binding regions summary]] | ||
| + | *[[File:Binding-regions-ChIP-Seq-characteristics-distribution-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]] | ||
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*[[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: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]] | *[[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]] | ||
| + | *[[File:Binding-regions-Create-matrix-by-mixture-of-normal-components-(ChIP-seq)-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:Binding-regions-Distinct-TF-classes-icon.png]] [[Distinct TF classes (analysis)|Distinct TF classes]] | *[[File:Binding-regions-Distinct-TF-classes-icon.png]] [[Distinct TF classes (analysis)|Distinct TF classes]] | ||
| + | *[[File:BSA-Extract-ribosomal-RNA-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]] | ||
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*[[File:Binding-regions-IPS-prediction-icon.png]] [[IPS prediction (analysis)|IPS prediction]] | *[[File:Binding-regions-IPS-prediction-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]] | ||
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*[[File:Binding-regions-Merge-binding-regions-for-cell-lines-icon.png]] [[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]] | ||
*[[File:BSA-Merge-track-statistics-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]] | *[[File:BSA-Merge-track-statistics-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]] | ||
Revision as of 17:43, 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:
- 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:
Reference types
Reference types defined in this plugin:
-icon.png){kind=link}
