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• • Abhi@abhinav

  

  Abhi answered the question Why bioinformatics is important ? 539 days ago

  Bioinformatics is an interdisciplinary field that combines biology, computer science, statistics, and mathematics to analyze and interpret biological data. It plays a crucial role in advancing our understanding of biological processes, enabling...
• • Abhi@abhinav

  

  Abhi answered the question Do we need any ethical clearance to work in SARS-CoV2 data ? 539 days ago

  Working with SARS-CoV-2 data, especially data related to human subjects, often involves sensitive information and potential privacy concerns. The need for ethical clearance or approval depends on the specific context and the nature of the research...
• • Abhi@abhinav

  

  Abhi bookmarked Metabuli 분리 improves metagenomic read classification 571 days ago

  Metabuli 분리 improves metagenomic read classification through metamers, DNA-AA k-mers, to be sensitive and specific, recovering 99% and 98% of DNA or AA classifiers.   Metabuli is metagenomic classifier that jointly analyze both DNA and amino...

  https://github.com/steineggerlab/Metabuli
• • Abhi@abhinav

  

  Abhi bookmarked homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes 571 days ago

  This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more...

  https://github.com/wf8/homologizer
• • LEGE@lege

  

  LEGE bookmarked Genome Context Viewer (GCV) 584 days ago

  The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses functional annotations as a unit of search and comparison. By adopting a common set of annotations, data-store...

  https://github.com/legumeinfo/gcv
• • LEGE@lege

  

  LEGE bookmarked Tools for id conversion 585 days ago

  g:Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces. We provide at least 40 types of IDs for more than 60 species. The 98 different namespaces supported for human include Ensembl,...

  https://biit.cs.ut.ee/gprofiler/convert
• • LEGE@lege

  

  LEGE bookmarked Proksee: in-depth characterization and visualization of bacterial genomes 596 days ago

  Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

  https://proksee.ca/
• • LEGE@lege

  

  LEGE posted to the wire 597 days ago

  https://hplgit.github.io/bioinf-py/doc/pub/html/main_bioinf.html #Learn #Python #Bioinformatics
• • Abhi@abhinav

  

  Abhi bookmarked OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes 604 days ago

  OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...

  https://orthovenn3.bioinfotoolkits.net/
• • Abhi@abhinav

  

  Abhi bookmarked JBrowse 2: a modular genome browser with views of synteny and structural variation 610 days ago

  igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests) jb2-web - stock...

  https://github.com/GMOD/jb2profile
• • Abhi@abhinav

  

  Abhi posted to the wire 610 days ago

  Nice #Upset #plot tutorial https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions
• • Abhi@abhinav

  

  Abhi bookmarked genomenotebook 615 days ago

  https://dbikard.github.io/genomenotebook/ Install pip install genomenotebook How to use Create a simple genome browser with a search bar. The sequence appears when zooming in. import genomenotebook as gn g=gn.GenomeBrowser(genome_path,...

  https://dbikard.github.io/genomenotebook/
• • Abhi@abhinav

  

  Abhi answered the question Do we need any ethical clearance to work in SARS-CoV2 data ? 626 days ago

  While SARS-CoV-2 data handling may not be directly associated with humans, it is important to remember that this data often includes personal and sensitive information about individuals, such as their health status, medical history, and demographic...
• • LEGE@lege

  

  LEGE asked Do we need any ethical clearance to work in SARS-CoV2 data ? 626 days ago
• • LEGE@lege

  

  LEGE bookmarked Carrot2 clustering engine 628 days ago

    This is the demo application of the Carrot2 clustering engine. It uses Carrot2's algorithms to organize search results into thematic folders. User interfaces Web Search Clustering organizes search results from public...

  https://search.carrot2.org/#/search/web
• • LEGE@lege

  

  LEGE bookmarked Research Rabbit 628 days ago

  You’re determined students, passionate teachers, and inspired creators of everything we know! Yet, all the researchers we spoke with over the past year uncovered the same reality: Despite the degrees you’ve earned, the effort and...

  https://researchrabbitapp.com/
• • LEGE@lege

  

  LEGE commented on the blog Basic command-line to run BLAST 632 days ago

  Understanding the parameters  https://www.arabidopsis.org/Blast/BLASToptions.jsp
• • BioStar@biostar

  

  BioStar posted a new ad in the Opportunity Opportunity at McDermott Center Bioinformatics Lab 634 days ago
• • BioStar@biostar

  

  BioStar bookmarked gget 634 days ago

  gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of...

  https://github.com/pachterlab/gget
• • BioStar@biostar

  

  BioStar bookmarked Upset plots ! 642 days ago

  Upset plots are a type of visualization used to analyze the intersection of sets or categories. They are particularly useful for displaying data with multiple categories and analyzing their overlaps. In an upset plot, each row represents a category...

  https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions

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