Difference between revisions of "Data mining"

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#[[GFF2 features|GFF2 features]] - ''Descriptions of features contained in the WormBase GFF2 genome annotation files''
 
#[[GFF2 features|GFF2 features]] - ''Descriptions of features contained in the WormBase GFF2 genome annotation files''
  
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== Query Languages ==
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== WormMine ==
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[[ WormMine | Link to documentation]]
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== SimpleMine ==
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SimpleMine User's Guide: https://wiki.wormbase.org/index.php/UserGuide:SimpleMine
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== RNASeq Related Tools ==
  
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#[[Data mining:AQL tutorial|AQL tutorial]] - ''Using the AceDB query language, AQL''  -- DEPRECATED: moved to new site
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SPELL: Clustering analyses for microarray, tiling array, and RNASeq expression. https://spell.wormbase.org/ Documentation: https://wiki.wormbase.org/index.php/SPELL
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#[[Data mining:WQL tutorial|WQL tutorial]] - ''Using the WormBase query language, WQL'' -- DEPRECATED: moved to new site
 
  
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== WormMine ==
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Expression Dataset Locator: https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi
  
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[[ WormMine | Link to documentation]]
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RNAseq FPKM Download: https://wormbase.org/tools/rnaseq/fpkmmine.cgi
  
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== WormMart  ==
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RNASeq FPKM Graphs: Graphs derived from ModENCODE can be located under the Expression Widget of Gene pages. Documentation: https://wiki.wormbase.org/index.php/UserGuide:RNASeqFPKMGraph
  
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#[[Data mining:WormMart|WormMart]]
 
  
 
== APIs  ==
 
== APIs  ==
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#[[Mining AceDB/WormBase with AcePerl|Mining AceDB/WormBase with AcePerl]]
 
#[[Mining AceDB/WormBase with AcePerl|Mining AceDB/WormBase with AcePerl]]
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== Query Languages  ==
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 +
#[[Data mining:AQL tutorial|AQL tutorial]] - ''Using the AceDB query language, AQL''  -- DEPRECATED: moved to new site
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#[[Data mining:WQL tutorial|WQL tutorial]] - ''Using the WormBase query language, WQL'' -- DEPRECATED: moved to new site
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=== Bio::DB::GFF  ===
 
=== Bio::DB::GFF  ===

Latest revision as of 01:36, 1 April 2022

Data Model

  1. About the WormBase data model - how data is stored and structured at WormBase
  2. AceDB classes - A comprehensive list of AceDB classes
  3. AceDB classes tutorial -Examples and descriptions of commonly accessed classes at WormBase
  4. GFF2 features - Descriptions of features contained in the WormBase GFF2 genome annotation files

WormMine

Link to documentation

SimpleMine

SimpleMine User's Guide: https://wiki.wormbase.org/index.php/UserGuide:SimpleMine

RNASeq Related Tools

SPELL: Clustering analyses for microarray, tiling array, and RNASeq expression. https://spell.wormbase.org/ Documentation: https://wiki.wormbase.org/index.php/SPELL

Expression Dataset Locator: https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi

RNAseq FPKM Download: https://wormbase.org/tools/rnaseq/fpkmmine.cgi

RNASeq FPKM Graphs: Graphs derived from ModENCODE can be located under the Expression Widget of Gene pages. Documentation: https://wiki.wormbase.org/index.php/UserGuide:RNASeqFPKMGraph


APIs

AcePerl, a Perl interface to AceDB/WormBase

  1. Mining AceDB/WormBase with AcePerl


Query Languages

  1. AQL tutorial - Using the AceDB query language, AQL -- DEPRECATED: moved to new site
  2. WQL tutorial - Using the WormBase query language, WQL -- DEPRECATED: moved to new site


Bio::DB::GFF

  1. Mining WormBase with Bio::DB::GFF - extract sequence annotations en masse using this Perl module

Miscellaneous

  1. Linking To WormBase
  2. Converting Coordinates between releases
  3. WormBase Identifiers - A quick guide to WormBase object identifiers
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