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:
 +
*[[File:Default-analysis-icon.png]] [[Blast alignment coverage (analysis)|Blast alignment coverage]]
 
*[[File:BSA-ChIP-seq-peak-profile-icon.png]] [[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]]
 
*[[File:BSA-ChIP-seq-peak-profile-icon.png]] [[ChIP-seq peak profile (analysis)|ChIP-seq peak profile]]
 
*[[File:BSA-Change-profile-cutoffs-icon.png]] [[Change profile cutoffs (analysis)|Change profile cutoffs]]
 
*[[File:BSA-Change-profile-cutoffs-icon.png]] [[Change profile cutoffs (analysis)|Change profile cutoffs]]
 
*[[File:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]]
 
*[[File:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]]
 +
*[[File:BSA-Cluster-track-icon.png]] [[Cluster track (analysis)|Cluster track]]
 +
*[[File:Default-analysis-icon.png]] [[Color space to nucleotide (analysis)|Color space to nucleotide]]
 +
*[[File:BSA-Compare-TFBS-mutations-icon.png]] [[Compare TFBS mutations (analysis)|Compare TFBS mutations]]
 
*[[File:Default-analysis-icon.png]] [[Compare site models (analysis)|Compare site models]]
 
*[[File:Default-analysis-icon.png]] [[Compare site models (analysis)|Compare site models]]
 
*[[File:BSA-Construct-IPS-CisModule-icon.png]] [[Construct IPS CisModule (analysis)|Construct IPS CisModule]]
 
*[[File:BSA-Construct-IPS-CisModule-icon.png]] [[Construct IPS CisModule (analysis)|Construct IPS CisModule]]
 
*[[File:BSA-Convert-site-models-to-proteins-icon.png]] [[Convert site models to proteins (analysis)|Convert site models to proteins]]
 
*[[File:BSA-Convert-site-models-to-proteins-icon.png]] [[Convert site models to proteins (analysis)|Convert site models to proteins]]
 +
*[[File:BSA-Convert-site-search-summary-icon.png]] [[Convert site search summary (analysis)|Convert site search summary]]
 
*[[File:BSA-Convert-table-to-track-icon.png]] [[Convert table to track (analysis)|Convert table to track]]
 
*[[File:BSA-Convert-table-to-track-icon.png]] [[Convert table to track (analysis)|Convert table to track]]
 
*[[File:BSA-Create-IPS-model-icon.png]] [[Create IPS model (analysis)|Create IPS model]]
 
*[[File:BSA-Create-IPS-model-icon.png]] [[Create IPS model (analysis)|Create IPS model]]
 
*[[File:BSA-Create-Match-model-icon.png]] [[Create Match model (analysis)|Create Match model]]
 
*[[File:BSA-Create-Match-model-icon.png]] [[Create Match model (analysis)|Create Match model]]
 
*[[File:BSA-Create-profile-from-gene-table-icon.png]] [[Create profile from gene table (analysis)|Create profile from gene table]]
 
*[[File:BSA-Create-profile-from-gene-table-icon.png]] [[Create profile from gene table (analysis)|Create profile from gene table]]
*[[File:BSA-Create-profile-from-table-icon.png]] [[Create profile from table (analysis)|Create profile from 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]]
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*[[File:Default-analysis-icon.png]] [[MicroRNA finder (analysis)|MicroRNA finder]]
 
*[[File:Default-analysis-icon.png]] [[MicroRNA finder (analysis)|MicroRNA finder]]
 
*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]]
 
*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]]
*[[File:Default-analysis-icon.png]] [[Preprocess raw reads (analysis)|Preprocess raw reads]]
+
*[[File:BSA-Mutation-effect-on-sites-icon.png]] [[Mutation effect on sites (analysis)|Mutation effect on sites]]
 +
*[[File:BSA-Preprocess-raw-reads-icon.png]] [[Preprocess raw reads (analysis)|Preprocess raw reads]]
 
*[[File:BSA-Process-track-with-sites-icon.png]] [[Process track with sites (analysis)|Process track with sites]]
 
*[[File:BSA-Process-track-with-sites-icon.png]] [[Process track with sites (analysis)|Process track with sites]]
*[[File:Default-analysis-icon.png]] [[Read counter (analysis)|Read counter]]
+
*[[File:BSA-Remove-overlapping-sites-icon.png]] [[Remove overlapping sites (analysis)|Remove overlapping sites]]
 
*[[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]]
 
*[[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]]
 
*[[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]]
 
*[[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]]
*[[File:BSA-SNP-matching-icon.png]] [[SNP matching (analysis)|SNP matching]]
 
 
*[[File:Default-analysis-icon.png]] [[Site counts in repeats (analysis)|Site counts in repeats]]
 
*[[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-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-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-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: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]] [[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:Default-analysis-icon.png]] [[Track coverage (analysis)|Track coverage]]
*[[File:Default-analysis-icon.png]] [[Track statistics (analysis)|Track statistics]]
+
*[[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 ===
 
=== Importers ===
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*[[EMBL format|EMBL format (*.embl)]]
 
*[[EMBL format|EMBL format (*.embl)]]
 
*[[Fasta format|Fasta format (*.fasta)]]
 
*[[Fasta format|Fasta format (*.fasta)]]
*[[Fastq as track (file format)|Fastq as track (*.fastq)]]
 
 
*[[Fastq format|Fastq format (*.fastq)]]
 
*[[Fastq format|Fastq format (*.fastq)]]
 
*[[GenBank format|GenBank format (*.gb)]]
 
*[[GenBank format|GenBank format (*.gb)]]

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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