Difference between revisions of "Ru.biosoft.bsa (plugin)"
From BioUML platform
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:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
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=== Analysis methods === | === Analysis methods === | ||
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*[[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-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]] [[Double encode SOLiD (analysis)|Double encode SOLiD]] | ||
*[[File:Default-analysis-icon.png]] [[Extract RNA length (analysis)|Extract RNA length]] | *[[File:Default-analysis-icon.png]] [[Extract RNA length (analysis)|Extract RNA length]] | ||
*[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]] | *[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]] | ||
Revision as of 12:22, 25 August 2015
- ID
- ru.biosoft.bsa
- Name
- Bio-sequences analyses plugin
- Provider
- Institute of Systems Biology
- Version
- 0.9.9
Contents |
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
- Double encode SOLiD
- 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:
