Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
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*[[Change profile cutoffs (analysis)|Change profile cutoffs]] | *[[Change profile cutoffs (analysis)|Change profile cutoffs]] | ||
*[[Chromosome enrichment (analysis)|Chromosome enrichment]] | *[[Chromosome enrichment (analysis)|Chromosome enrichment]] | ||
| + | *[[Cis-module identification (analysis)|Cis-module identification]] | ||
*[[Compare site models (analysis)|Compare site models]] | *[[Compare site models (analysis)|Compare site models]] | ||
*[[Construct IPS CisModule (analysis)|Construct IPS CisModule]] | *[[Construct IPS CisModule (analysis)|Construct IPS CisModule]] | ||
*[[Convert site models to proteins (analysis)|Convert site models to proteins]] | *[[Convert site models to proteins (analysis)|Convert site models to proteins]] | ||
*[[Convert table to track (analysis)|Convert table to track]] | *[[Convert table to track (analysis)|Convert table to track]] | ||
| + | *[[Count olig frequencies (analysis)|Count olig frequencies]] | ||
*[[Create IPS model (analysis)|Create IPS model]] | *[[Create IPS model (analysis)|Create IPS model]] | ||
*[[Create Match model (analysis)|Create Match model]] | *[[Create Match model (analysis)|Create Match model]] | ||
| + | *[[Create matrix by mixture of normal components (analysis)|Create matrix by mixture of normal components]] | ||
*[[Create profile from gene table (analysis)|Create profile from gene table]] | *[[Create profile from gene table (analysis)|Create profile from gene table]] | ||
*[[Create profile from table (analysis)|Create profile from table]] | *[[Create profile from table (analysis)|Create profile from table]] | ||
| Line 39: | Line 42: | ||
*[[Merge track statistics (analysis)|Merge track statistics]] | *[[Merge track statistics (analysis)|Merge track statistics]] | ||
*[[MicroRNA aligner (analysis)|MicroRNA aligner]] | *[[MicroRNA aligner (analysis)|MicroRNA aligner]] | ||
| + | *[[Mixture of normal components (analysis)|Mixture of normal components]] | ||
*[[Motif quality analysis]] | *[[Motif quality analysis]] | ||
*[[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] | *[[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] | ||
Revision as of 17:42, 7 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
- Cis-module identification
- Compare site models
- Construct IPS CisModule
- Convert site models to proteins
- Convert table to track
- Count olig frequencies
- Create IPS model
- Create Match model
- Create matrix by mixture of normal components
- 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
- Mixture of normal components
- 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:
