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-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]] | ||
| + | *[[File:BSA-Cluster-track-icon.png]] [[Cluster track (analysis)|Cluster track]] | ||
| + | *[[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]] | ||
*[[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: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-site-model-table-icon.png]] [[Create profile from site model table (analysis)|Create profile from site model 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:Default-analysis-icon.png]] [[Double encode SOLiD (analysis)|Double encode SOLiD]] | ||
*[[File:Default-analysis-icon.png]] [[Extract RNA length (analysis)|Extract RNA length]] | *[[File:Default-analysis-icon.png]] [[Extract RNA length (analysis)|Extract RNA length]] | ||
*[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]] | *[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]] | ||
| Line 36: | Line 42: | ||
*[[File:Default-analysis-icon.png]] [[MicroRNA finder (analysis)|MicroRNA finder]] | *[[File:Default-analysis-icon.png]] [[MicroRNA finder (analysis)|MicroRNA finder]] | ||
*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | *[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]] | ||
| − | *[[File: | + | *[[File:BSA-Mutation-effect-on-sites-icon.png]] [[Mutation effect on sites (analysis)|Mutation effect on sites]] |
| + | *[[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-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]] | ||
| − | |||
*[[File:Default-analysis-icon.png]] [[Site counts in repeats (analysis)|Site counts in repeats]] | *[[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-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]] | ||
| + | *[[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]] [[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:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]] | ||
| − | *[[File: | + | *[[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 58: | 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)]] | ||
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:
