Ru.biosoft.bsa (plugin)
From BioUML platform
- ID
- ru.biosoft.bsa
- Name
- Bio-sequences analyses plugin
- Provider
- Institute of Systems Biology
- Version
- 0.9.10
Contents[hide] |
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 TFBS mutations
Compare site models
Construct IPS CisModule
Convert site models to proteins
Convert site search summary
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
Remove overlapping sites
Run MACS 1_3_7 on ChiP-Seq
Run MACS 1_4_0 on ChiP-Seq
Site counts in repeats
Site search on gene set
Site search on track
Site search report
Site search result optimization
Site search summary
Sort SQL track
Split fasta
Stem loop predictor
Track correlation
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 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: