Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
(Add analyses list) |
(Importers list added) |
||
| Line 35: | Line 35: | ||
*[[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]] |
*[[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]] | ||
| Line 49: | Line 49: | ||
*[[Track coverage (analysis)|Track coverage]] | *[[Track coverage (analysis)|Track coverage]] | ||
*[[Track statistics (analysis)|Track statistics]] | *[[Track statistics (analysis)|Track statistics]] | ||
| + | |||
| + | === Importers === | ||
| + | Data element importers defined in this plugin: | ||
| + | *[[BED format|BED format (*.bed)]] | ||
| + | *[[Breakdancer output (file format)|Breakdancer output (*.ctx)]] | ||
| + | *[[CNVnator genotype output (file format)|CNVnator genotype output (*.genotype)]] | ||
| + | *[[EMBL format|EMBL format (*.embl)]] | ||
| + | *[[Fasta format|Fasta format (*.fasta)]] | ||
| + | *[[Fastq as track (file format)|Fastq as track (*.fastq)]] | ||
| + | *[[Fastq format|Fastq format (*.fastq)]] | ||
| + | *[[GenBank format|GenBank format (*.gb)]] | ||
| + | *[[Gene Transfer Format|Gene Transfer Format (*.gtf)]] | ||
| + | *[[General Feature Format|General Feature Format (*.gff)]] | ||
| + | *[[Interval format|Interval format (*.interval)]] | ||
| + | *[[Pindel output (file format)|Pindel output]] | ||
| + | *[[SAM or BAM alignment file|SAM or BAM alignment file (*.sam, *.bam)]] | ||
| + | *[[SISSRs output (file format)|SISSRs output (*.bsites)]] | ||
| + | *[[VAT output (file format)|VAT output (*.vat)]] | ||
| + | *[[VCF format|VCF format (*.vcf)]] | ||
| + | *[[Varscan output (file format)|Varscan output]] | ||
| + | *[[Wiggle format|Wiggle format (*.wig)]] | ||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Revision as of 13:58, 7 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 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)
