Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
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*[[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]] | *[[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]] | ||
*[[Analysis of SNPs and Binding sites (analysis)|Analysis of SNPs and Binding sites]] | *[[Analysis of SNPs and Binding sites (analysis)|Analysis of SNPs and Binding sites]] | ||
| + | *[[Analysis of five site models (analysis)|Analysis of five site models]] | ||
| + | *[[Binding regions summary (analysis)|Binding regions summary]] | ||
*[[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]] | *[[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]] | ||
*[[Change profile cutoffs (analysis)|Change profile cutoffs]] | *[[Change profile cutoffs (analysis)|Change profile cutoffs]] | ||
| Line 28: | Line 30: | ||
*[[Filter track by condition (analysis)|Filter track by condition]] | *[[Filter track by condition (analysis)|Filter track by condition]] | ||
*[[GC island finder (analysis)|GC island finder]] | *[[GC island finder (analysis)|GC island finder]] | ||
| + | *[[Gathering genome statistics (analysis)|Gathering genome statistics]] | ||
*[[Gene set to track (analysis)|Gene set to track]] | *[[Gene set to track (analysis)|Gene set to track]] | ||
*[[Genome coverage (analysis)|Genome coverage]] | *[[Genome coverage (analysis)|Genome coverage]] | ||
| Line 33: | Line 36: | ||
*[[IPS motif discovery (analysis)|IPS motif discovery]] | *[[IPS motif discovery (analysis)|IPS motif discovery]] | ||
*[[Join tracks (analysis)|Join tracks]] | *[[Join tracks (analysis)|Join tracks]] | ||
| + | *[[Merge binding regions for cell-lines (analysis)|Merge binding regions for cell-lines]] | ||
*[[Merge track statistics (analysis)|Merge track statistics]] | *[[Merge track statistics (analysis)|Merge track statistics]] | ||
*[[MicroRNA aligner (analysis)|MicroRNA aligner]] | *[[MicroRNA aligner (analysis)|MicroRNA aligner]] | ||
*[[Motif quality analysis]] | *[[Motif quality analysis]] | ||
| + | *[[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] | ||
*[[Preprocess raw reads (analysis)|Preprocess raw reads]] | *[[Preprocess raw reads (analysis)|Preprocess raw reads]] | ||
*[[Process track with sites (analysis)|Process track with sites]] | *[[Process track with sites (analysis)|Process track with sites]] | ||
Revision as of 17:18, 6 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:
- Analysis of Binding Regions
- Analysis of Cis-Regulatory Modules
- Analysis of SNPs and Binding sites
- Analysis of five site models
- Binding regions summary
- 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
- Filter one track by another
- Filter track by condition
- GC island finder
- Gathering genome statistics
- Gene set to track
- Genome coverage
- Heterozygous site caller
- IPS motif discovery
- Join tracks
- Merge binding regions for cell-lines
- Merge track statistics
- MicroRNA aligner
- Motif quality analysis
- Non-merged ChIP-Seq tracks summary
- 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:
