Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
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*[[Varscan output (file format)|Varscan output]] | *[[Varscan output (file format)|Varscan output]] | ||
*[[Wiggle format|Wiggle format (*.wig)]] | *[[Wiggle format|Wiggle format (*.wig)]] | ||
| + | |||
| + | === Reference types === | ||
| + | [[Reference type]]s defined in this plugin: | ||
| + | *[[File:ReferenceType-SNPTableType-icon.png]] [[SNP (reference type)|SNP]] | ||
| + | *[[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]] | ||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:ISB plugins]] | [[Category:ISB plugins]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Revision as of 18:20, 14 May 2013
- ID
- ru.biosoft.bsa
- Name
- Bio-sequences analyses plugin
- Provider
- Institute of Systems Biology
- Version
- 0.9.4
Analysis methods
Analysis methods defined in this plugin:
- Analysis of Binding Regions
- Analysis of Cis-Regulatory Modules
- Analysis of SNPs and Binding sites
- 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
- Gene set to track
- Genome coverage
- Heterozygous site caller
- IPS motif discovery
- Join tracks
- Merge track statistics
- MicroRNA aligner
- Motif quality analysis
- 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)
Reference types
Reference types defined in this plugin:
