Data

Tools

Indexes

Applications

Experiments

Open Source Science

bedsect

BedSect web server source code repository.

https://github.com/sraghav-lab/bedsect

Science Score: 31.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.7%) to scientific vocabulary

Keywords

bioinformatics bioinformatics-tool chip-seq genomic-regions multiple-datasets webserver
Last synced: 6 months ago · JSON representation ·

Repository

BedSect web server source code repository.

Basic Info
  • Host: GitHub
  • Owner: sraghav-lab
  • License: gpl-3.0
  • Language: PHP
  • Default Branch: master
  • Homepage: http://imgsb.org/bedsect/
  • Size: 2.57 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
bioinformatics bioinformatics-tool chip-seq genomic-regions multiple-datasets webserver
Created almost 8 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

alt text

Bedsect is a web server tool for overlapping genomic regions from multiple datasets.

Please check the Insatallation Manual for more details.

Support

If you have any suugesation, feature request or found a bug, please write us at imgsb [at] ils.res.in.

Citation

If you use Bedsect, please cite the following paper.

Bedsect: An integrated web server application to perform intersection, visualization and functional annotation of genomic regions from multiple datasets Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil Kumar Raghav Front. Genet.; doi: https://doi.org/10.3389/fgene.2020.00003

fair-software.eu

Owner

  • Name: Immunogenomics & Systems Bio. Lab
  • Login: sraghav-lab
  • Kind: organization
  • Location: India

Immunogenomics & System Bio. Lab @ Institute of Life Sciences, Bhubaneswar.

Citation (CITATION.bib) 

@ARTICLE{10.3389/fgene.2020.00003,
  
AUTHOR={Mishra, Gyan Prakash and Ghosh, Arup and Jha, Atimukta and Raghav, Sunil Kumar},   
	 
TITLE={BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets},      
	
JOURNAL={Frontiers in Genetics},      
	
VOLUME={11},      

PAGES={3},     
	
YEAR={2020},      
	  
URL={https://www.frontiersin.org/article/10.3389/fgene.2020.00003},       
	
DOI={10.3389/fgene.2020.00003},      
	
ISSN={1664-8021},   
   
ABSTRACT={A large number of genomic regions, such as transcription factor binding sites (TFBSs) captured from next generation sequencing (NGS) data analyses or those available from the public resource database ENCODE, are generally overlapped to answer a variety of biological questions. Though several command-line tools are available to perform such an analysis, there is a notable lack of an integrated webserver application with which to identify genomic region intersections, generate publication-ready plots depicting subsets of the overlapped regions, and perform functional annotation. Thus, there is an ardent need for a comprehensive and user-friendly webserver application that allows the users to either upload multiple datasets or select from the integrated Gene Transcription Regulation Database (GTRD). We thus introduce BedSect (http://imgsb.org/bedsect/.), which not only fulfils the above criteria but also performs intersection analysis along with visualization of the intersection regions as an UpSet and correlation plot using the integrated Shiny application. Moreover, analyses, including functional annotation, gene ontology, and biological pathways enrichment for the identified unique and intersected genomic regions, can also be performed using the integrated GREAT tool. To view the genomic regions in the genome browser, the inbuilt hyperlink for UCSC can redirect the user to visualize the results as custom tracks.}
}

GitHub Events

Total
Last Year

Dependencies

application/email/composer.json packagist
  • doctrine/annotations 1.2.* development
  • friendsofphp/php-cs-fixer ^2.2 development
  • phpdocumentor/phpdocumentor 2.* development
  • phpunit/phpunit ^4.8 || ^5.7 development
  • zendframework/zend-eventmanager 3.0.* development
  • zendframework/zend-i18n 2.7.3 development
  • zendframework/zend-serializer 2.7.* development
  • ext-ctype *
  • php >=5.5.0