Difference between revisions of "FlyBase:FlyBase Help Index"
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| + | == '''New to Flies''' == | ||
| + | |||
| + | '''Useful Guides for Drosophila Research''' | ||
| + | *[[FlyBase:New_to_Flies | New to Flies links]] | ||
| + | |||
| + | == '''Tweetorials''' == | ||
| + | |||
| + | '''Topic-specific FlyBase Tweetorials''' | ||
| + | *[[FlyBase:Tweetorial | All Tweetorials]] | ||
== '''Video Tutorials''' == | == '''Video Tutorials''' == | ||
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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= | + | *[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] | ||
*[https://www.youtube.com/watch?v=jgCON15SiRo Finding related genes/alleles in FlyBase: Vocabularies] | *[https://www.youtube.com/watch?v=jgCON15SiRo Finding related genes/alleles in FlyBase: Vocabularies] | ||
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'''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= | + | *[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] | ||
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*[https://www.youtube.com/watch?v=16SGlcASOL4 How to cite FlyBase] | *[https://www.youtube.com/watch?v=16SGlcASOL4 How to cite FlyBase] | ||
| − | == ''' | + | == '''Report Help''' == |
| − | |||
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| − | |||
| − | |||
| − | |||
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'''Field by Field guides to FlyBase Reports''' | '''Field by Field guides to FlyBase Reports''' | ||
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*[[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]] | ||
| + | *[[FlyBase:Chemical | Chemical Report]] | ||
*[[FlyBase:Clone Report | Clone Report]] | *[[FlyBase:Clone Report | Clone Report]] | ||
| + | *[[FlyBase:Vocabularies | CV (Controlled Vocabulary) Term Report]] | ||
| + | *[[FlyBase:Dataset-Collection Report | Dataset/Collection Report]] | ||
| + | *[[FlyBase:Experimental Tool | Experimental Tool Report]] | ||
*[[FlyBase:Gene Report | Gene Report]] | *[[FlyBase:Gene Report | Gene Report]] | ||
| + | *[[FlyBase:Gene Group Report | Gene Group Report]] | ||
*[[FlyBase:Human Disease Report | Human Disease Model Report]] | *[[FlyBase:Human Disease Report | Human Disease Model Report]] | ||
*[[FlyBase:Image Report | Image Report]] | *[[FlyBase:Image Report | Image Report]] | ||
*[[FlyBase:Insertion Report | Insertion Report]] | *[[FlyBase:Insertion Report | Insertion Report]] | ||
*[[FlyBase:Interaction Report | Interaction Report]] | *[[FlyBase:Interaction Report | Interaction Report]] | ||
| − | |||
*[[FlyBase:Natural Transposon Report | Natural Transposon Report]] | *[[FlyBase:Natural Transposon Report | Natural Transposon Report]] | ||
| − | *[[FlyBase: | + | *[[FlyBase:Pathway_Report | Pathway 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]] | ||
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*[[FlyBase:Stock Report | Stock Report]] | *[[FlyBase:Stock Report | Stock Report]] | ||
*[[FlyBase:Transcript Report | Transcript Report]] | *[[FlyBase:Transcript Report | Transcript Report]] | ||
| − | |||
| − | + | *[[FlyBase:Computed cytological data | Computed Cytological data]] | |
| − | *[[FlyBase:Computed cytological data | Computed Cytological | + | |
| − | + | == '''Curation Documentation''' == | |
| − | + | *[[FlyBase:Controlled vocabularies used by FlyBase | Controlled Vocabularies used by FlyBase]] | |
| − | *[[FlyBase: | + | *[[FlyBase:Gene Model Annotation Guidelines | Gene Model Annotation Guidelines]] |
| + | *[[FlyBase:Gene Ontology (GO) Annotation | Gene Ontology (GO) Annotation]] | ||
| + | *[[FlyBase:Nontraditional alleles | Nontraditional alleles]] | ||
| + | *[[FlyBase:Vectors and Constructs | Comonly used Vectors and Constructs]] | ||
| − | == '''Tools Documentation''' == | + | == '''Tools and Downloads Documentation''' == |
'''Tools Overview''' | '''Tools Overview''' | ||
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''' | ''' | ||
*[[FlyBase:Tools_Overview#Jump_to_Gene | Jump to Gene]] | *[[FlyBase:Tools_Overview#Jump_to_Gene | Jump to Gene]] | ||
| − | *[ | + | *[[FlyBase:QueryBuilder Help | QueryBuilder]] |
*[[FlyBase:QuickSearch | QuickSearch]] | *[[FlyBase:QuickSearch | QuickSearch]] | ||
| − | *[ | + | *[[FlyBase:Vocabularies Tool | Vocabularies Tool]] |
| − | '''Genomic/Map | + | '''Genomic/Map Tools Help |
| + | ''' | ||
| + | * [[FlyBase:Tools_Overview#BLAST | BLAST]] | ||
| + | * [[FlyBase:CytoSearch | CytoSearch]] | ||
| + | * [[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 | ||
''' | ''' | ||
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* [[FlyBase:GBrowse | FlyBase GBrowse Help]] | * [[FlyBase:GBrowse | FlyBase GBrowse Help]] | ||
* [[FlyBase:GBrowse Tracks | GBrowse Tracks]] | * [[FlyBase:GBrowse Tracks | GBrowse Tracks]] | ||
| − | * [[FlyBase:JBrowse | FlyBase | + | * [[FlyBase:Differences between JBrowse and GBrowse on FlyBase | Feature differences between JBrowse and GBrowse on FlyBase]] |
| − | * [[FlyBase:JBrowse | + | * [[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''' | ||
| − | * [ | + | * [[FlyBase:Batch Download | Batch Download]] |
| − | * Coordinate Converter | + | * [[FlyBase:Coordinate Converter | Coordinate Converter]] |
| − | * ID Converter | + | * [[FlyBase:ID_Converter | ID Converter ]] |
| − | * Sequence Downloader | + | * [[FlyBase:SequenceDownloader | Sequence Downloader ]] |
'''RNA-Seq Tools Help''' | '''RNA-Seq Tools Help''' | ||
| − | *[ | + | * [[FlyBase:RNA-Seq Overview | RNA-Seq Overview]] |
| − | *[http:// | + | * [http://{{flybaseorg}}/rnaseq/region RNA-Seq by Region] |
| − | *[http:// | + | * [http://{{flybaseorg}}/rnaseq/profile_search RNA-Seq Profile] |
| − | *[http:// | + | * [http://{{flybaseorg}}/rnaseq/simsearch RNA-Seq Similarity] |
| − | == ''' | + | '''Downloads''' |
| + | *[[FlyBase:Downloads Overview | Downloads Overview]] | ||
| + | |||
| + | == '''Information for Authors''' == | ||
*[[FlyBase:Author Guidelines | Author Guidelines]] | *[[FlyBase:Author Guidelines | Author Guidelines]] | ||
| − | *[[FlyBase: | + | *[[FlyBase:About#Citing_FlyBase | Citing FlyBase]] |
| + | *[[FlyBase:Fast Track Your Paper | Fast Track Your Paper]] | ||
| + | *[http://beta.flybase.org/community FlyBase Community] | ||
| + | *[[FlyBase:Gene Snapshots | Gene Snapshots]] | ||
*[[FlyBase:Nomenclature | Nomenclature]] | *[[FlyBase:Nomenclature | Nomenclature]] | ||
*[[FlyBase:Personal communications to FlyBase | Personal Communications to FlyBase]] | *[[FlyBase:Personal communications to FlyBase | Personal Communications to FlyBase]] | ||
| + | |||
| + | == '''Other Help''' == | ||
| + | |||
| + | *[[FlyBase:FAQ | FlyBase FAQ]] | ||
| + | *[[FlyBase:Links to and from FlyBase | Links to and from FlyBase]] | ||
| + | *[[FlyBase:FlyBase Website Access Fee FAQ | FlyBase Website Access Fee FAQ]] | ||
| + | *[[FlyBase:Community Advisory Group | FlyBase Community Advisory Group]] | ||
| + | *[[FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters | FlyBase Guides: Pamphlets, Powerpoints, and Posters]] | ||
| + | *[[FlyBase:Fly Board| Fly Board]] | ||
| + | *[[FlyBase:Papers with technical advances | Papers with technical advances]] | ||
| + | *[[FlyBase:CitationAndGuides | Papers to cite when using FlyBase]] | ||
Latest revision as of 16:26, 11 January 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
- Natural Transposon Report
- Pathway Report
- Polypeptide Report
- Recombinant Construct Report
- Reference Report
- Sequence Feature 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