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-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:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]] | *[[File:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]] | ||
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*[[File:Default-analysis-icon.png]] [[Compare site models (analysis)|Compare site models]] | *[[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]] | ||
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*[[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]] | ||
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*[[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]] | ||
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*[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]] | *[[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:Default-analysis-icon.png]] [[GC island finder (analysis)|GC island finder]] | *[[File:Default-analysis-icon.png]] [[GC island finder (analysis)|GC island finder]] | ||
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*[[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:Default-analysis-icon.png]] [[Genome coverage (analysis)|Genome coverage]] | *[[File:Default-analysis-icon.png]] [[Genome coverage (analysis)|Genome coverage]] | ||
*[[File:Default-analysis-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]] | *[[File:Default-analysis-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]] | ||
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*[[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]] | ||
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*[[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:Default-analysis-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]] | *[[File:Default-analysis-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]] | ||
*[[File:Default-analysis-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]] | *[[File:Default-analysis-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]] | ||
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*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | *[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | ||
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*[[File:Default-analysis-icon.png]] [[Preprocess raw reads (analysis)|Preprocess raw reads]] | *[[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]] | ||
Revision as of 13:40, 17 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:
ChIP-seq peak profile
Change profile cutoffs
Chromosome enrichment
- Compare site models
Construct IPS CisModule
Convert site models to proteins
Convert table to track
Create IPS model
Create Match model
Create profile from gene table
Create profile from table
Create weight matrix model
- Extract ribosomal RNA
Filter one track by another
Filter track by condition
- GC island finder
Gene set to track
- Genome coverage
- Heterozygous site caller
IPS motif discovery
Join tracks
- Merge track statistics
- MicroRNA aligner
Motif quality analysis
- 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:
