Difference between revisions of "Ru.biosoft.bsa (plugin)"

Revision as of 16:03, 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 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)