Ru.biosoft.bsa (plugin)
From BioUML platform
Revision as of 18:09, 14 June 2013 by BioUML wiki Bot (Talk | contribs)
- 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 Cis-Regulatory Modules
Analysis of SNPs and Binding sites
Analysis of five site models
Binding regions summary
ChIP-Seq characteristics distribution
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 matrix by mixture of normal components (ChIP-seq)
Create profile from gene table
Create profile from table
Create weight matrix model
Distinct TF classes
Extract ribosomal RNA
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 ROC-curves
IPS motif discovery
IPS prediction
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: