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

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:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Version
 
;Version
:0.9.4
+
:0.9.10
  
 
=== Analysis methods ===
 
=== Analysis methods ===
 
Analysis methods defined in this plugin:
 
Analysis methods defined in this plugin:
*[[Analysis of Binding Regions (analysis)|Analysis of Binding Regions]]
+
*[[File:Default-analysis-icon.png]] [[Blast alignment coverage (analysis)|Blast alignment coverage]]
*[[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]]
+
*[[File:BSA-ChIP-seq-peak-profile-icon.png]] [[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]]
*[[Analysis of SNPs and Binding sites (analysis)|Analysis of SNPs and Binding sites]]
+
*[[File:BSA-Change-profile-cutoffs-icon.png]] [[Change profile cutoffs (analysis)|Change profile cutoffs]]
*[[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]]
+
*[[File:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]]
*[[Change profile cutoffs (analysis)|Change profile cutoffs]]
+
*[[File:BSA-Cluster-track-icon.png]] [[Cluster track (analysis)|Cluster track]]
*[[Chromosome enrichment (analysis)|Chromosome enrichment]]
+
*[[File:Default-analysis-icon.png]] [[Color space to nucleotide (analysis)|Color space to nucleotide]]
*[[Compare site models (analysis)|Compare site models]]
+
*[[File:BSA-Compare-TFBS-mutations-icon.png]] [[Compare TFBS mutations (analysis)|Compare TFBS mutations]]
*[[Construct IPS CisModule (analysis)|Construct IPS CisModule]]
+
*[[File:Default-analysis-icon.png]] [[Compare site models (analysis)|Compare site models]]
*[[Convert site models to proteins (analysis)|Convert site models to proteins]]
+
*[[File:BSA-Construct-IPS-CisModule-icon.png]] [[Construct IPS CisModule (analysis)|Construct IPS CisModule]]
*[[Convert table to track (analysis)|Convert table to track]]
+
*[[File:BSA-Convert-site-models-to-proteins-icon.png]] [[Convert site models to proteins (analysis)|Convert site models to proteins]]
*[[Create IPS model (analysis)|Create IPS model]]
+
*[[File:BSA-Convert-site-search-summary-icon.png]] [[Convert site search summary (analysis)|Convert site search summary]]
*[[Create Match model (analysis)|Create Match model]]
+
*[[File:BSA-Convert-table-to-track-icon.png]] [[Convert table to track (analysis)|Convert table to track]]
*[[Create profile from gene table (analysis)|Create profile from gene table]]
+
*[[File:BSA-Create-IPS-model-icon.png]] [[Create IPS model (analysis)|Create IPS model]]
*[[Create profile from table (analysis)|Create profile from table]]
+
*[[File:BSA-Create-Match-model-icon.png]] [[Create Match model (analysis)|Create Match model]]
*[[Create weight matrix model (analysis)|Create weight matrix model]]
+
*[[File:BSA-Create-profile-from-gene-table-icon.png]] [[Create profile from gene table (analysis)|Create profile from gene table]]
*[[Filter one track by another (analysis)|Filter one track by another]]
+
*[[File:BSA-Create-profile-from-site-model-table-icon.png]] [[Create profile from site model table (analysis)|Create profile from site model table]]
*[[Filter track by condition (analysis)|Filter track by condition]]
+
*[[File:BSA-Create-weight-matrix-model-icon.png]] [[Create weight matrix model (analysis)|Create weight matrix model]]
*[[GC island finder (analysis)|GC island finder]]
+
*[[File:Default-analysis-icon.png]] [[Double encode SOLiD (analysis)|Double encode SOLiD]]
*[[Gene set to track (analysis)|Gene set to track]]
+
*[[File:Default-analysis-icon.png]] [[Extract RNA length (analysis)|Extract RNA length]]
*[[Genome coverage (analysis)|Genome coverage]]
+
*[[File:Default-analysis-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]]
*[[Heterozygous site caller (analysis)|Heterozygous site caller]]
+
*[[File:BSA-Filter-one-track-by-another-icon.png]] [[Filter one track by another (analysis)|Filter one track by another]]
*[[IPS motif discovery (analysis)|IPS motif discovery]]
+
*[[File:BSA-Filter-track-by-condition-icon.png]] [[Filter track by condition (analysis)|Filter track by condition]]
*[[Join tracks (analysis)|Join tracks]]
+
*[[File:Default-analysis-icon.png]] [[GC island finder (analysis)|GC island finder]]
*[[Merge track statistics (analysis)|Merge track statistics]]
+
*[[File:BSA-Gene-set-to-track-icon.png]] [[Gene set to track (analysis)|Gene set to track]]
*[[MicroRNA aligner (analysis)|MicroRNA aligner]]
+
*[[File:Default-analysis-icon.png]] [[Genome coverage (analysis)|Genome coverage]]
*[[Motif quality analysis|Motif quality analysis]]
+
*[[File:Default-analysis-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]]
*[[Preprocess raw reads (analysis)|Preprocess raw reads]]
+
*[[File:BSA-IPS-motif-discovery-icon.png]] [[IPS motif discovery (analysis)|IPS motif discovery]]
*[[Process track with sites (analysis)|Process track with sites]]
+
*[[File:BSA-Join-tracks-icon.png]] [[Join tracks (analysis)|Join tracks]]
*[[Read counter (analysis)|Read counter]]
+
*[[File:Default-analysis-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]]
*[[Run MACS 1.3.7 on ChiP-Seq (analysis)|Run MACS 1_3_7 on ChiP-Seq]]
+
*[[File:Default-analysis-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]]
*[[Run MACS 1.4.0 on ChiP-Seq (analysis)|Run MACS 1_4_0 on ChiP-Seq]]
+
*[[File:Default-analysis-icon.png]] [[MicroRNA finder (analysis)|MicroRNA finder]]
*[[SNP matching (analysis)|SNP matching]]
+
*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]]
*[[Site counts in repeats (analysis)|Site counts in repeats]]
+
*[[File:BSA-Mutation-effect-on-sites-icon.png]] [[Mutation effect on sites (analysis)|Mutation effect on sites]]
*[[Site search on gene set (analysis)|Site search on gene set]]
+
*[[File:BSA-Preprocess-raw-reads-icon.png]] [[Preprocess raw reads (analysis)|Preprocess raw reads]]
*[[Site search on track (analysis)|Site search on track]]
+
*[[File:BSA-Process-track-with-sites-icon.png]] [[Process track with sites (analysis)|Process track with sites]]
*[[Site search result optimization (analysis)|Site search result optimization]]
+
*[[File:BSA-Remove-overlapping-sites-icon.png]] [[Remove overlapping sites (analysis)|Remove overlapping sites]]
*[[Site search summary (analysis)|Site search summary]]
+
*[[File:BSA-Run-MACS-1.3.7-on-ChiP-Seq-icon.png]] [[Run MACS 1.3.7 on ChiP-Seq (analysis)|Run MACS 1_3_7 on ChiP-Seq]]
*[[Track coverage (analysis)|Track coverage]]
+
*[[File:BSA-Run-MACS-1.4.0-on-ChiP-Seq-icon.png]] [[Run MACS 1.4.0 on ChiP-Seq (analysis)|Run MACS 1_4_0 on ChiP-Seq]]
*[[Track statistics (analysis)|Track statistics]]
+
*[[File:Default-analysis-icon.png]] [[Site counts in repeats (analysis)|Site counts in repeats]]
 +
*[[File:BSA-Site-search-on-gene-set-icon.png]] [[Site search on gene set (analysis)|Site search on gene set]]
 +
*[[File:BSA-Site-search-on-track-icon.png]] [[Site search on track (analysis)|Site search on track]]
 +
*[[File:BSA-Site-search-report-icon.png]] [[Site search report (analysis)|Site search report]]
 +
*[[File:BSA-Site-search-result-optimization-icon.png]] [[Site search result optimization (analysis)|Site search result optimization]]
 +
*[[File:BSA-Site-search-summary-icon.png]] [[Site search summary (analysis)|Site search summary]]
 +
*[[File:Default-analysis-icon.png]] [[Sort SQL track (analysis)|Sort SQL track]]
 +
*[[File:Default-analysis-icon.png]] [[Split fasta (analysis)|Split fasta]]
 +
*[[File:Default-analysis-icon.png]] [[Stem loop predictor (analysis)|Stem loop predictor]]
 +
*[[File:Default-analysis-icon.png]] [[Track correlation (analysis)|Track correlation]]
 +
*[[File:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]]
 +
*[[File:BSA-Track-statistics-icon.png]] [[Track statistics (analysis)|Track statistics]]
 +
*[[File:BSA-Transcript-set-to-track-icon.png]] [[Transcript set to track (analysis)|Transcript set to track]]
 +
 
 +
=== Importers ===
 +
Data element importers for the following file formats are 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 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)]]
 +
 
 +
=== Host objects ===
 +
JavaScript [[Host object (extension point)|host objects]] defined in this plugin:
 +
*[[Bsa (host object)|bsa]]
 +
*[[SiteAnalysis (host object)|siteAnalysis]]
 +
 
 +
=== Reference types ===
 +
[[Reference type]]s defined in this plugin:
 +
*[[File:ReferenceType-MatrixTableType-icon.png]] [[Matrices (reference type)|Matrices]]
 +
*[[File:ReferenceType-TransfacMatrixTableType-icon.png]] [[Matrices - TRANSFAC|Matrices: TRANSFAC]]
 +
*[[File:ReferenceType-TransfacProteinType-icon.png]] [[Proteins - Transfac|Proteins: Transfac]]
 +
*[[File:ReferenceType-SNPTableType-icon.png]] [[SNP (reference type)|SNP]]
  
 
[[Category:Plugins]]
 
[[Category:Plugins]]
 +
[[Category:ISB plugins]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 16:35, 12 March 2019

ID
ru.biosoft.bsa
Name
Bio-sequences analyses plugin
Provider
Institute of Systems Biology
Version
0.9.10

Contents

[edit] Analysis methods

Analysis methods defined in this plugin:

[edit] Importers

Data element importers for the following file formats are defined in this plugin:

[edit] Host objects

JavaScript host objects defined in this plugin:

[edit] Reference types

Reference types defined in this plugin:

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