Difference between revisions of "Ru.biosoft.bsa (plugin)"
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:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Version | ;Version | ||
| − | :0.9. | + | :0.9.10 |
=== Analysis methods === | === Analysis methods === | ||
Analysis methods defined in this plugin: | Analysis methods defined in this plugin: | ||
| − | *[[ | + | *[[File:Default-analysis-icon.png]] [[Blast alignment coverage (analysis)|Blast alignment coverage]] |
| − | + | *[[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:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]] | |
| − | *[[Change profile cutoffs (analysis)|Change profile cutoffs]] | + | *[[File:BSA-Cluster-track-icon.png]] [[Cluster track (analysis)|Cluster track]] |
| − | *[[Chromosome enrichment (analysis)|Chromosome enrichment]] | + | *[[File:Default-analysis-icon.png]] [[Color space to nucleotide (analysis)|Color space to nucleotide]] |
| − | *[[Compare site models (analysis)|Compare site models]] | + | *[[File:BSA-Compare-TFBS-mutations-icon.png]] [[Compare TFBS mutations (analysis)|Compare TFBS mutations]] |
| − | *[[Construct IPS CisModule (analysis)|Construct IPS CisModule]] | + | *[[File:Default-analysis-icon.png]] [[Compare site models (analysis)|Compare site models]] |
| − | *[[Convert site models to proteins (analysis)|Convert site models to proteins]] | + | *[[File:BSA-Construct-IPS-CisModule-icon.png]] [[Construct IPS CisModule (analysis)|Construct IPS CisModule]] |
| − | *[[Convert table to track (analysis)|Convert table to track]] | + | *[[File:BSA-Convert-site-models-to-proteins-icon.png]] [[Convert site models to proteins (analysis)|Convert site models to proteins]] |
| − | *[[Create IPS model (analysis)|Create IPS model]] | + | *[[File:BSA-Convert-site-search-summary-icon.png]] [[Convert site search summary (analysis)|Convert site search summary]] |
| − | *[[Create Match model (analysis)|Create Match model]] | + | *[[File:BSA-Convert-table-to-track-icon.png]] [[Convert table to track (analysis)|Convert table to track]] |
| − | *[[Create profile from gene table (analysis)|Create profile from gene table]] | + | *[[File:BSA-Create-IPS-model-icon.png]] [[Create IPS model (analysis)|Create IPS model]] |
| − | *[[Create profile from table (analysis)|Create profile from table]] | + | *[[File:BSA-Create-Match-model-icon.png]] [[Create Match model (analysis)|Create Match model]] |
| − | *[[Create weight matrix model (analysis)|Create weight matrix model]] | + | *[[File:BSA-Create-profile-from-gene-table-icon.png]] [[Create profile from gene table (analysis)|Create profile from gene table]] |
| − | *[[Filter one track by another (analysis)|Filter one track by another]] | + | *[[File:BSA-Create-profile-from-site-model-table-icon.png]] [[Create profile from site model table (analysis)|Create profile from site model table]] |
| − | *[[Filter track by condition (analysis)|Filter track by condition]] | + | *[[File:BSA-Create-weight-matrix-model-icon.png]] [[Create weight matrix model (analysis)|Create weight matrix model]] |
| − | *[[GC island finder (analysis)|GC island finder]] | + | *[[File:Default-analysis-icon.png]] [[Double encode SOLiD (analysis)|Double encode SOLiD]] |
| − | *[[Gene set to track (analysis)|Gene set to track]] | + | *[[File:Default-analysis-icon.png]] [[Extract RNA length (analysis)|Extract RNA length]] |
| − | *[[Genome coverage (analysis)|Genome coverage]] | + | *[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]] |
| − | *[[Heterozygous site caller (analysis)|Heterozygous site caller]] | + | *[[File:BSA-Filter-one-track-by-another-icon.png]] [[Filter one track by another (analysis)|Filter one track by another]] |
| − | *[[IPS motif discovery (analysis)|IPS motif discovery]] | + | *[[File:BSA-Filter-track-by-condition-icon.png]] [[Filter track by condition (analysis)|Filter track by condition]] |
| − | *[[Join tracks (analysis)|Join tracks]] | + | *[[File:Default-analysis-icon.png]] [[GC island finder (analysis)|GC island finder]] |
| − | *[[Merge track statistics (analysis)|Merge track statistics]] | + | *[[File:BSA-Gene-set-to-track-icon.png]] [[Gene set to track (analysis)|Gene set to track]] |
| − | *[[MicroRNA aligner (analysis)|MicroRNA aligner]] | + | *[[File:Default-analysis-icon.png]] [[Genome coverage (analysis)|Genome coverage]] |
| − | *[[Motif quality analysis]] | + | *[[File:Default-analysis-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]] |
| − | *[[Preprocess raw reads (analysis)|Preprocess raw reads]] | + | *[[File:BSA-IPS-motif-discovery-icon.png]] [[IPS motif discovery (analysis)|IPS motif discovery]] |
| − | *[[Process track with sites (analysis)|Process track with sites]] | + | *[[File:BSA-Join-tracks-icon.png]] [[Join tracks (analysis)|Join tracks]] |
| − | *[[ | + | *[[File:Default-analysis-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]] |
| − | *[[Run MACS 1.3.7 on ChiP-Seq (analysis)|Run MACS 1_3_7 on ChiP-Seq]] | + | *[[File:Default-analysis-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]] |
| − | *[[Run MACS 1.4.0 on ChiP-Seq (analysis)|Run MACS 1_4_0 on ChiP-Seq]] | + | *[[File:Default-analysis-icon.png]] [[MicroRNA finder (analysis)|MicroRNA finder]] |
| − | *[[ | + | *[[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]] | |
| − | *[[Site search on gene set (analysis)|Site search on gene set]] | + | *[[File:BSA-Preprocess-raw-reads-icon.png]] [[Preprocess raw reads (analysis)|Preprocess raw reads]] |
| − | *[[Site search on track (analysis)|Site search on track]] | + | *[[File:BSA-Process-track-with-sites-icon.png]] [[Process track with sites (analysis)|Process track with sites]] |
| − | *[[Site search result optimization (analysis)|Site search result optimization]] | + | *[[File:BSA-Remove-overlapping-sites-icon.png]] [[Remove overlapping sites (analysis)|Remove overlapping sites]] |
| − | *[[Site search summary (analysis)|Site search summary]] | + | *[[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]] |
| − | *[[Track coverage (analysis)|Track coverage]] | + | *[[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]] |
| − | *[[Track statistics (analysis)|Track statistics]] | + | *[[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-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-summary-icon.png]] [[Site search summary (analysis)|Site search summary]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Sort SQL track (analysis)|Sort SQL track]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Split fasta (analysis)|Split fasta]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Stem loop predictor (analysis)|Stem loop predictor]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Track correlation (analysis)|Track correlation]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]] | ||
| + | *[[File:BSA-Track-statistics-icon.png]] [[Track statistics (analysis)|Track statistics]] | ||
| + | *[[File:BSA-Transcript-set-to-track-icon.png]] [[Transcript set to track (analysis)|Transcript set to track]] | ||
=== Importers === | === Importers === | ||
| Line 57: | Line 69: | ||
*[[EMBL format|EMBL format (*.embl)]] | *[[EMBL format|EMBL format (*.embl)]] | ||
*[[Fasta format|Fasta format (*.fasta)]] | *[[Fasta format|Fasta format (*.fasta)]] | ||
| − | |||
*[[Fastq format|Fastq format (*.fastq)]] | *[[Fastq format|Fastq format (*.fastq)]] | ||
*[[GenBank format|GenBank format (*.gb)]] | *[[GenBank format|GenBank format (*.gb)]] | ||
| Line 70: | Line 81: | ||
*[[Varscan output (file format)|Varscan output]] | *[[Varscan output (file format)|Varscan output]] | ||
*[[Wiggle format|Wiggle format (*.wig)]] | *[[Wiggle format|Wiggle format (*.wig)]] | ||
| + | |||
| + | === Host objects === | ||
| + | JavaScript [[Host object (extension point)|host objects]] defined in this plugin: | ||
| + | *[[Bsa (host object)|bsa]] | ||
| + | *[[SiteAnalysis (host object)|siteAnalysis]] | ||
| + | |||
| + | === Reference types === | ||
| + | [[Reference type]]s defined in this plugin: | ||
| + | *[[File:ReferenceType-MatrixTableType-icon.png]] [[Matrices (reference type)|Matrices]] | ||
| + | *[[File:ReferenceType-TransfacMatrixTableType-icon.png]] [[Matrices - TRANSFAC|Matrices: 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:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 16:35, 12 March 2019
- ID
- ru.biosoft.bsa
- Name
- Bio-sequences analyses plugin
- Provider
- Institute of Systems Biology
- Version
- 0.9.10
Contents |
[edit] 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
Remove overlapping sites
Run MACS 1_3_7 on ChiP-Seq
Run MACS 1_4_0 on ChiP-Seq
- Site counts in repeats
Site search on gene set
Site search on track
Site search report
Site search result optimization
Site search summary
- Sort SQL track
- Split fasta
- Stem loop predictor
- Track correlation
- Track coverage
Track statistics
Transcript set to track
[edit] 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 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)
[edit] Host objects
JavaScript host objects defined in this plugin:
[edit] Reference types
Reference types defined in this plugin:
