Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
||
| Line 6: | Line 6: | ||
:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Version | ;Version | ||
| − | :0.9. | + | :0.9.8 |
=== 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]] | ||
| Line 22: | Line 23: | ||
*[[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]] [[Extract RNA length (analysis)|Extract RNA length]] | *[[File:Default-analysis-icon.png]] [[Extract RNA length (analysis)|Extract RNA length]] | ||
| Line 38: | Line 39: | ||
*[[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:BSA-Mutation-effect-on-sites-icon.png]] [[Mutation effect on sites (analysis)|Mutation effect on sites]] | ||
*[[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]] | ||
*[[File:Default-analysis-icon.png]] [[Read counter (analysis)|Read counter]] | *[[File:Default-analysis-icon.png]] [[Read counter (analysis)|Read counter]] | ||
| + | *[[File:Default-analysis-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]] | ||
| Line 53: | Line 56: | ||
*[[File:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]] | *[[File:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]] | ||
*[[File:Default-analysis-icon.png]] [[Track statistics (analysis)|Track statistics]] | *[[File:Default-analysis-icon.png]] [[Track statistics (analysis)|Track statistics]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Transcript set to track (analysis)|Transcript set to track]] | ||
=== Importers === | === Importers === | ||
Revision as of 16:20, 11 December 2014
- ID
- ru.biosoft.bsa
- Name
- Bio-sequences analyses plugin
- Provider
- Institute of Systems Biology
- Version
- 0.9.8
Contents[hide] |
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 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 site model table
Create weight matrix model
- 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 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:
