Difference between revisions of "FlyBase:FlyBase Help Index"
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'''Tools series | '''Tools series | ||
''' | ''' | ||
| − | *[https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq Part I: Using GBrowse] | + | *[https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq Part I: Using GBrowse] -- <span style="color:red"> Warning: The GBrowse genome viewer has been updated to JBrowse, but techniques shown here are still useful in JBrowse.</span> |
*[https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=17s RNA-Seq Part II: Using RNA-Seq Profile Search] | *[https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=17s RNA-Seq Part II: Using RNA-Seq Profile Search] | ||
*[https://www.youtube.com/watch?v=mcMpRxeX-KY RNA Seq Part III: Searching for Similarly Expressed Genes] | *[https://www.youtube.com/watch?v=mcMpRxeX-KY RNA Seq Part III: Searching for Similarly Expressed Genes] | ||
| Line 36: | Line 36: | ||
'''RNA-Seq series | '''RNA-Seq series | ||
''' | ''' | ||
| − | *[https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq Part I: Using GBrowse] | + | *[https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq Part I: Using GBrowse] -- <span style="color:red"> Warning: The GBrowse genome viewer has been updated to JBrowse, but techniques shown here are still useful in JBrowse.</span> |
*[https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=17s RNA-Seq Part II: Using RNA-Seq Profile Search] | *[https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=17s RNA-Seq Part II: Using RNA-Seq Profile Search] | ||
*[https://www.youtube.com/watch?v=mcMpRxeX-KY RNA Seq Part III: Searching for Similarly Expressed Genes] | *[https://www.youtube.com/watch?v=mcMpRxeX-KY RNA Seq Part III: Searching for Similarly Expressed Genes] | ||
| Line 53: | Line 53: | ||
*[[FlyBase:Balancer/Genotype variant Report | Balancer/Genotype variant Report]] | *[[FlyBase:Balancer/Genotype variant Report | Balancer/Genotype variant Report]] | ||
*[[FlyBase:Cell Line Report | Cell Line Report]] | *[[FlyBase:Cell Line Report | Cell Line Report]] | ||
| − | *[[Chemical | + | *[[FlyBase:Chemical | Chemical Report]] |
*[[FlyBase:Clone Report | Clone Report]] | *[[FlyBase:Clone Report | Clone Report]] | ||
*[[FlyBase:Vocabularies | CV (Controlled Vocabulary) Term Report]] | *[[FlyBase:Vocabularies | CV (Controlled Vocabulary) Term Report]] | ||
| Line 64: | Line 64: | ||
*[[FlyBase:Insertion Report | Insertion Report]] | *[[FlyBase:Insertion Report | Insertion Report]] | ||
*[[FlyBase:Interaction Report | Interaction Report]] | *[[FlyBase:Interaction Report | Interaction Report]] | ||
| + | *[[FlyBase:Macromolecular Complex Report | Macromolecular Complex Report]] | ||
| + | *[[FlyBase:Metabolic_Pathway_Report | Metabolic Pathway Report]] | ||
*[[FlyBase:Natural Transposon Report | Natural Transposon Report]] | *[[FlyBase:Natural Transposon Report | Natural Transposon Report]] | ||
| − | |||
*[[FlyBase:Polypeptide Report | Polypeptide Report]] | *[[FlyBase:Polypeptide Report | Polypeptide Report]] | ||
*[[FlyBase:Recombinant Construct Report | Recombinant Construct Report]] | *[[FlyBase:Recombinant Construct Report | Recombinant Construct Report]] | ||
*[[FlyBase:Reference Report | Reference Report]] | *[[FlyBase:Reference Report | Reference Report]] | ||
*[[FlyBase:Sequence Feature Report | Sequence Feature Report]] | *[[FlyBase:Sequence Feature Report | Sequence Feature Report]] | ||
| + | *[[FlyBase:Signaling_Pathway_Report | Signaling Pathway Report]] | ||
*[[FlyBase:Strain Report | Strain Report]] | *[[FlyBase:Strain Report | Strain Report]] | ||
*[[FlyBase:Stock Report | Stock Report]] | *[[FlyBase:Stock Report | Stock Report]] | ||
| Line 98: | Line 100: | ||
'''Genomic/Map Tools Help | '''Genomic/Map Tools Help | ||
''' | ''' | ||
| − | * BLAST | + | * [[FlyBase:Tools_Overview#BLAST | BLAST]] |
* [[FlyBase:CytoSearch | CytoSearch]] | * [[FlyBase:CytoSearch | CytoSearch]] | ||
* [[FlyBase:Feature Mapper | Feature Mapper]] | * [[FlyBase:Feature Mapper | Feature Mapper]] | ||
| + | * [[FlyBase:JBrowse | FlyBase JBrowse Help]] | ||
| + | * [[FlyBase:JBrowse Tracks | JBrowse Tracks]] | ||
| + | * [[FlyBase:modENCODE data at FlyBase | modENCODE data at FlyBase]] | ||
| + | |||
| + | '''Tools for Archived Instances of FlyBase earlier than FB2022_05 | ||
| + | ''' | ||
* [[FlyBase:GBrowse | FlyBase GBrowse Help]] | * [[FlyBase:GBrowse | FlyBase GBrowse Help]] | ||
* [[FlyBase:GBrowse Tracks | GBrowse Tracks]] | * [[FlyBase:GBrowse Tracks | GBrowse Tracks]] | ||
| − | |||
| − | |||
* [[FlyBase:Differences between JBrowse and GBrowse on FlyBase | Feature differences between JBrowse and GBrowse on FlyBase]] | * [[FlyBase:Differences between JBrowse and GBrowse on FlyBase | Feature differences between JBrowse and GBrowse on FlyBase]] | ||
* [[FlyBase:Complete list of GBrowse/JBrowse Track Differences | Complete list of GBrowse/JBrowse Data Track Differences]] | * [[FlyBase:Complete list of GBrowse/JBrowse Track Differences | Complete list of GBrowse/JBrowse Data Track Differences]] | ||
| − | + | * [[FlyBase:Using FTP Archives | Using FTP Archives]] | |
'''Retrieve/Convert Tools Help''' | '''Retrieve/Convert Tools Help''' | ||
| Line 136: | Line 142: | ||
== '''Other Help''' == | == '''Other Help''' == | ||
| + | *[[FlyBase:FAQ | FlyBase FAQ]] | ||
*[[FlyBase:Links to and from FlyBase | Links to and from FlyBase]] | *[[FlyBase:Links to and from FlyBase | Links to and from FlyBase]] | ||
*[[FlyBase:FlyBase Website Access Fee FAQ | FlyBase Website Access Fee FAQ]] | *[[FlyBase:FlyBase Website Access Fee FAQ | FlyBase Website Access Fee FAQ]] | ||
| Line 142: | Line 149: | ||
*[[FlyBase:Fly Board| Fly Board]] | *[[FlyBase:Fly Board| Fly Board]] | ||
*[[FlyBase:Papers with technical advances | Papers with technical advances]] | *[[FlyBase:Papers with technical advances | Papers with technical advances]] | ||
| + | *[[FlyBase:CitationAndGuides | Papers to cite when using FlyBase]] | ||
Revision as of 12:37, 5 December 2024
New to Flies
Useful Guides for Drosophila Research
Tweetorials
Topic-specific FlyBase Tweetorials
Video Tutorials
- FlyBase Video Tutorials on YouTube organized into four playlists.
Basic navigation series
- How to find all data related to a gene
- How to generate an excel file of all alleles of a gene
- Finding related genes in FlyBase: Gene Groups
- Finding related genes/alleles in FlyBase: Vocabularies
- Finding related genes in FlyBase: The Gene Ontology
- Gene Snapshots in FlyBase
- Finding genes with similar phenotypes
Tools series
- RNA-Seq Part I: Using GBrowse -- Warning: The GBrowse genome viewer has been updated to JBrowse, but techniques shown here are still useful in JBrowse.
- RNA-Seq Part II: Using RNA-Seq Profile Search
- RNA Seq Part III: Searching for Similarly Expressed Genes
- Finding related genes/alleles in FlyBase: Vocabularies
- Using the Orthology search tool
- Finding related genes in FlyBase: The Gene Ontology
- Finding genes with similar phenotypes
RNA-Seq series
- RNA-Seq Part I: Using GBrowse -- Warning: The GBrowse genome viewer has been updated to JBrowse, but techniques shown here are still useful in JBrowse.
- RNA-Seq Part II: Using RNA-Seq Profile Search
- RNA Seq Part III: Searching for Similarly Expressed Genes
FlyBase Guidelines
Report Help
Field by Field guides to FlyBase Reports
- All Reports
- Aberration Report
- Allele Report
- Balancer/Genotype variant Report
- Cell Line Report
- Chemical Report
- Clone Report
- CV (Controlled Vocabulary) Term Report
- Dataset/Collection Report
- Experimental Tool Report
- Gene Report
- Gene Group Report
- Human Disease Model Report
- Image Report
- Insertion Report
- Interaction Report
- Macromolecular Complex Report
- Metabolic Pathway Report
- Natural Transposon Report
- Polypeptide Report
- Recombinant Construct Report
- Reference Report
- Sequence Feature Report
- Signaling Pathway Report
- Strain Report
- Stock Report
- Transcript Report
Curation Documentation
- Controlled Vocabularies used by FlyBase
- Gene Model Annotation Guidelines
- Gene Ontology (GO) Annotation
- Nontraditional alleles
- Comonly used Vectors and Constructs
Tools and Downloads Documentation
Tools Overview
Query Tools Help
Genomic/Map Tools Help
Tools for Archived Instances of FlyBase earlier than FB2022_05
- FlyBase GBrowse Help
- GBrowse Tracks
- Feature differences between JBrowse and GBrowse on FlyBase
- Complete list of GBrowse/JBrowse Data Track Differences
- Using FTP Archives
Retrieve/Convert Tools Help
RNA-Seq Tools Help
Downloads
Information for Authors
- Author Guidelines
- Citing FlyBase
- Fast Track Your Paper
- FlyBase Community
- Gene Snapshots
- Nomenclature
- Personal Communications to FlyBase