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:BSA-Analysis-of-Cis-Regulatory-Modules-icon.png]] [[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]]
+
*[[File:Default-analysis-icon.png]] [[Blast alignment coverage (analysis)|Blast alignment coverage]]
−
*[[File:BSA-Analysis-of-SNPs-and-Binding-sites-icon.png]] [[Analysis of SNPs and Binding sites (analysis)|Analysis of SNPs and Binding sites]]
+
−
*[[File:BSA-Analysis-of-five-site-models-icon.png]] [[Analysis of five site models (analysis)|Analysis of five site models]]
+
−
*[[File:Binding-regions-Binding-regions-summary-icon.png]] [[Binding regions summary (analysis)|Binding regions summary]]
+
−
*[[File:Binding-regions-ChIP-Seq-characteristics-distribution-icon.png]] [[ChIP-Seq characteristics distribution (analysis)|ChIP-Seq characteristics distribution]]
+
 
*[[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:BSA-Chromosome-enrichment-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]]
+
*[[File:Default-analysis-icon.png]] [[Chromosome enrichment (analysis)|Chromosome enrichment]]
−
*[[File:Binding-regions-Cis-module-identification-icon.png]] [[Cis-module identification (analysis)|Cis-module identification]]
+
*[[File:BSA-Cluster-track-icon.png]] [[Cluster track (analysis)|Cluster track]]
−
*[[File:BSA-Compare-site-models-icon.png]] [[Compare site models (analysis)|Compare site models]]
+
*[[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: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:Binding-regions-Count-olig-frequencies-icon.png]] [[Count olig frequencies (analysis)|Count olig frequencies]]
 
 
*[[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:Binding-regions-Create-matrix-by-mixture-of-normal-components-icon.png]] [[Create matrix by mixture of normal components (analysis)|Create matrix by mixture of normal components]]
 
−
*[[File:Binding-regions-Create-matrix-by-mixture-of-normal-components-(ChIP-seq)-icon.png]] [[Create matrix by mixture of normal components (ChIP-seq) (analysis)|Create matrix by mixture of normal components (ChIP-seq)]]
 
 
*[[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:Binding-regions-Distinct-TF-classes-icon.png]] [[Distinct TF classes (analysis)|Distinct TF classes]]
+
*[[File:Default-analysis-icon.png]] [[Double encode SOLiD (analysis)|Double encode SOLiD]]
−
*[[File:BSA-Extract-ribosomal-RNA-icon.png]] [[Extract ribosomal RNA (analysis)|Extract ribosomal RNA]]
+
*[[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:BSA-Filter-one-track-by-another-icon.png]] [[Filter one track by another (analysis)|Filter one track by another]]
 
*[[File:BSA-Filter-one-track-by-another-icon.png]] [[Filter one track by another (analysis)|Filter one track by another]]
 
*[[File:BSA-Filter-track-by-condition-icon.png]] [[Filter track by condition (analysis)|Filter track by condition]]
 
*[[File:BSA-Filter-track-by-condition-icon.png]] [[Filter track by condition (analysis)|Filter track by condition]]
−
*[[File:BSA-GC-island-finder-icon.png]] [[GC island finder (analysis)|GC island finder]]
+
*[[File:Default-analysis-icon.png]] [[GC island finder (analysis)|GC island finder]]
−
*[[File:Binding-regions-Gathering-genome-statistics-icon.png]] [[Gathering genome statistics (analysis)|Gathering genome statistics]]
+
 
*[[File:BSA-Gene-set-to-track-icon.png]] [[Gene set to track (analysis)|Gene set to track]]
 
*[[File:BSA-Gene-set-to-track-icon.png]] [[Gene set to track (analysis)|Gene set to track]]
−
*[[File:BSA-Genome-coverage-icon.png]] [[Genome coverage (analysis)|Genome coverage]]
+
*[[File:Default-analysis-icon.png]] [[Genome coverage (analysis)|Genome coverage]]
−
*[[File:BSA-Heterozygous-site-caller-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]]
+
*[[File:Default-analysis-icon.png]] [[Heterozygous site caller (analysis)|Heterozygous site caller]]
−
*[[File:Binding-regions-IPS-ROC-curves-icon.png]] [[IPS ROC-curves (analysis)|IPS ROC-curves]]
+
 
*[[File:BSA-IPS-motif-discovery-icon.png]] [[IPS motif discovery (analysis)|IPS motif discovery]]
 
*[[File:BSA-IPS-motif-discovery-icon.png]] [[IPS motif discovery (analysis)|IPS motif discovery]]
−
*[[File:Binding-regions-IPS-prediction-icon.png]] [[IPS prediction (analysis)|IPS prediction]]
 
 
*[[File:BSA-Join-tracks-icon.png]] [[Join tracks (analysis)|Join tracks]]
 
*[[File:BSA-Join-tracks-icon.png]] [[Join tracks (analysis)|Join tracks]]
−
*[[File:Binding-regions-Merge-binding-regions-for-cell-lines-icon.png]] [[Merge binding regions for cell-lines (analysis)|Merge binding regions for cell-lines]]
+
*[[File:Default-analysis-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]]
−
*[[File:BSA-Merge-track-statistics-icon.png]] [[Merge track statistics (analysis)|Merge track statistics]]
+
*[[File:Default-analysis-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]]
−
*[[File:BSA-MicroRNA-aligner-icon.png]] [[MicroRNA aligner (analysis)|MicroRNA aligner]]
+
*[[File:Default-analysis-icon.png]] [[MicroRNA finder (analysis)|MicroRNA finder]]
−
*[[File:Binding-regions-Mixture-of-normal-components-icon.png]] [[Mixture of normal components (analysis)|Mixture of normal components]]
+
 
*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]]
 
*[[File:BSA-Motif-quality-analysis-icon.png]] [[Motif quality analysis]]
−
*[[File:Binding-regions-Non-merged-ChIP-Seq-tracks-summary-icon.png]] [[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]]
+
*[[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-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:BSA-Read-counter-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:BSA-Site-counts-in-repeats-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:BSA-Track-coverage-icon.png]] [[Track coverage (analysis)|Track coverage]]
+
*[[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-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:

Retrieved from "https://wiki.biouml.org/index.php?title=Ru.biosoft.bsa_(plugin)&oldid=7913"
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