Difference between revisions of "Data mining"
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#[[AceDB classes tutorial|AceDB classes tutorial]] -''Examples and descriptions of commonly accessed classes at WormBase'' | #[[AceDB classes tutorial|AceDB classes tutorial]] -''Examples and descriptions of commonly accessed classes at WormBase'' | ||
#[[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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== WormMine == | == WormMine == | ||
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== SimpleMine == | == SimpleMine == | ||
| − | + | SimpleMine User's Guide: https://wiki.wormbase.org/index.php/UserGuide:SimpleMine | |
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| + | == RNASeq Related Tools == | ||
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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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| + | Expression Dataset Locator: https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi | ||
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| + | RNAseq FPKM Download: https://wormbase.org/tools/rnaseq/fpkmmine.cgi | ||
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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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== 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 | ||
| + | #[[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
Contents
Data Model
- About the WormBase data model - how data is stored and structured at WormBase
- AceDB classes - A comprehensive list of AceDB classes
- AceDB classes tutorial -Examples and descriptions of commonly accessed classes at WormBase
- GFF2 features - Descriptions of features contained in the WormBase GFF2 genome annotation files
WormMine
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
Query Languages
- AQL tutorial - Using the AceDB query language, AQL -- DEPRECATED: moved to new site
- WQL tutorial - Using the WormBase query language, WQL -- DEPRECATED: moved to new site
Bio::DB::GFF
- Mining WormBase with Bio::DB::GFF - extract sequence annotations en masse using this Perl module
Miscellaneous
- Linking To WormBase
- Converting Coordinates between releases
- WormBase Identifiers - A quick guide to WormBase object identifiers
