Difference between revisions of "Data mining"
From WormBaseWiki
Jump to navigationJump to searchLine 5: | Line 5: | ||
#[[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'' | ||
− | |||
− | |||
− | |||
− | |||
− | |||
== WormMine == | == WormMine == | ||
Line 18: | Line 13: | ||
SimpleMine User's Guide: https://wiki.wormbase.org/index.php/UserGuide: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: | ||
+ | |||
+ | Expression Dataset Locator: | ||
+ | |||
+ | RNAseq FPKM Download: | ||
+ | |||
+ | RNASeq FPKM Graphs: | ||
+ | |||
== APIs == | == APIs == | ||
Line 24: | Line 30: | ||
#[[Mining AceDB/WormBase with AcePerl|Mining AceDB/WormBase with AcePerl]] | #[[Mining AceDB/WormBase with AcePerl|Mining AceDB/WormBase with AcePerl]] | ||
+ | |||
+ | |||
+ | == Query Languages == | ||
+ | |||
+ | #[[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 | ||
+ | |||
=== Bio::DB::GFF === | === Bio::DB::GFF === |
Revision as of 20:36, 31 March 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:
Expression Dataset Locator:
RNAseq FPKM Download:
RNASeq FPKM Graphs:
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