Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
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:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Version | ;Version | ||
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=== Analysis methods === | === Analysis methods === | ||
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*[[File:Default-analysis-icon.png]] [[Cluster track (analysis)|Cluster track]] | *[[File:Default-analysis-icon.png]] [[Cluster track (analysis)|Cluster track]] | ||
*[[File:Default-analysis-icon.png]] [[Color space to nucleotide (analysis)|Color space to nucleotide]] | *[[File:Default-analysis-icon.png]] [[Color space to nucleotide (analysis)|Color space to nucleotide]] | ||
| + | *[[File:BSA-Compare-TFBS-mutations-icon.png]] [[Compare TFBS mutations (analysis)|Compare TFBS mutations]] | ||
*[[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-site-search-summary-icon.png]] [[Convert site search summary (analysis)|Convert site search summary]] | ||
*[[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: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]] | ||
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*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | *[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | ||
*[[File:BSA-Mutation-effect-on-sites-icon.png]] [[Mutation effect on sites (analysis)|Mutation effect on sites]] | *[[File:BSA-Mutation-effect-on-sites-icon.png]] [[Mutation effect on sites (analysis)|Mutation effect on sites]] | ||
| − | *[[File: | + | *[[File:BSA-Preprocess-raw-reads-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:BSA-Read-counter-icon.png]] [[Read counter (analysis)|Read counter]] |
| − | *[[File: | + | *[[File:BSA-Remove-overlapping-sites-icon.png]] [[Remove overlapping sites (analysis)|Remove overlapping sites]] |
*[[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]] | ||
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*[[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-report-icon.png]] [[Site search report (analysis)|Site search report]] | ||
*[[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]] | ||
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*[[File:Default-analysis-icon.png]] [[Stem loop predictor (analysis)|Stem loop predictor]] | *[[File:Default-analysis-icon.png]] [[Stem loop predictor (analysis)|Stem loop predictor]] | ||
*[[File:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]] | *[[File:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]] | ||
| − | *[[File: | + | *[[File:BSA-Track-statistics-icon.png]] [[Track statistics (analysis)|Track statistics]] |
| − | *[[File: | + | *[[File:BSA-Transcript-set-to-track-icon.png]] [[Transcript set to track (analysis)|Transcript set to track]] |
=== Importers === | === Importers === | ||
Revision as of 19:03, 13 February 2017
- ID
- ru.biosoft.bsa
- Name
- Bio-sequences analyses plugin
- Provider
- Institute of Systems Biology
- Version
- 0.9.10
Contents |
Analysis methods
Analysis methods defined in this plugin:
Blast alignment coverage
ChIP-seq peak profile
Change profile cutoffs
- Chromosome enrichment
- Cluster track
- Color space to nucleotide
Compare TFBS mutations
- Compare site models
Construct IPS CisModule
Convert site models to proteins
Convert site search summary
Convert table to track
Create IPS model
Create Match model
Create profile from gene table
Create profile from site model table
Create weight matrix model
- Double encode SOLiD
- Extract RNA length
- 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
- MicroRNA finder
Motif quality analysis
Mutation effect on sites
Preprocess raw reads
Process track with sites
Read counter
Remove overlapping sites
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 report
Site search result optimization
Site search summary
- Split fasta
- Stem loop predictor
- Track coverage
Track statistics
Transcript set to track
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:
