Difference between revisions of "FlyBase:Drosophila Online Resources"

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* <b>cisTopic</b> Probabilistic modelling of cis-regulatory topics from single cell epigenomics data: <br />[https://github.com/aertslab/cisTopic/ cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium]
 
* <b>cisTopic</b> Probabilistic modelling of cis-regulatory topics from single cell epigenomics data: <br />[https://github.com/aertslab/cisTopic/ cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium]
 
* <b>DRscDB</b> DRSC scRNA-seq DataBase: <br />[https://www.flyrnai.org/tools/single_cell/ DRscDB, DRSC, Harvard Medical School, Boston, USA]
 
* <b>DRscDB</b> DRSC scRNA-seq DataBase: <br />[https://www.flyrnai.org/tools/single_cell/ DRscDB, DRSC, Harvard Medical School, Boston, USA]
* <b>SCEA</b> Single Cell Expression Atlas - Single Cell Gene Expression Across Species: <br />[https://www.ebi.ac.uk/gxa/sc SCEA< EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK]
+
* <b>SCEA</b> Single Cell Expression Atlas - Single Cell Gene Expression Across Species: <br />[https://www.ebi.ac.uk/gxa/sc SCEA EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK]
 
* <b>SCENIC</b> Single-Cell Regulatory Network Inference and Clustering <br />[https://github.com/aertslab/SCENIC SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium]
 
* <b>SCENIC</b> Single-Cell Regulatory Network Inference and Clustering <br />[https://github.com/aertslab/SCENIC SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium]
 
* <b>SCope</b> Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data <br />[https://github.com/aertslab/SCope SCope, VIB KU Leuven, Leuven, Belgium]
 
* <b>SCope</b> Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data <br />[https://github.com/aertslab/SCope SCope, VIB KU Leuven, Leuven, Belgium]

Revision as of 18:15, 10 February 2021

Atlases, Images and Videos

CRISPRs and TALENs

Data Repositories

Drosophila Genomes Data and Metadata

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Laboratory Resources

Miscellaneous

Non-coding (ncRNA) Databases and Tools

General

  • NONCODE, An integrated knowledge database dedicated to ncRNAs, especially lncRNAs (last updated 2017):
    NONCODE, Tsinghua University and Chinese Academy of Sciences, Beijing, China
  • NONCODE, Compiles data and annotations about non-coding RNAs for various species. NONCODE is an open repository curated from scientific literature and public databases which focuses mainly on long non-coding RNAs (lncRNAs). It intends to supply a detailed information for each entry encompassing sequence, structure, expression, function, conservation, or disease relevance. It also provides associated tools such as an ID converter and a blast tool:
    NONCODE, Multiple institutions, Beijing, China
  • Rfam, A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements (last updated 2017):
    Rfam, EMBL-EBI, Hinxton, UK
  • RNAcentral, Integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases (last updated 2017):
    RNAcentral, EMBL-EBI, Hinxton, UK

lncRNA

miRNA

General

NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.

miRNA Target Prediction

Validated miRNA Targets

Comparative miRNA Analysis

rRNA

tRNA

snoRNA

SRP RNA

Ontology Resources

Orthology Predictions

Phylogenetic Comparison Tools

Population Biology and Polymorphism Resources

Protein Analysis

Public Education

RNAi

Sequence Analysis

Single Cell RNA-seq

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource