BOL: Related items

Comparative genomics visualisation tools !

Neel — Thu, 17 Feb 2022 05:37:55 -0600

Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

CGView.js is a Circular Genome Viewing tool

LEGE — Wed, 27 Mar 2024 11:16:24 -0500

CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView.

CGView.js is the genome viewer of Proksee, an expert system for genome assembly, annotation and visualization.

Features

Circular and linear views of genomes
Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs
Smooth zooming down to the sequence level
Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)
Save high resolution PNG maps up to 8000x8000px
Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

LEGE — Tue, 10 Sep 2024 04:54:55 -0500

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

Synteny Portal: a web-based application portal for synteny block analysis

Jit — Wed, 24 May 2017 10:39:23 -0500

Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

http://bioinfo.konkuk.ac.kr/synteny_portal/

Address of the bookmark: http://bioinfo.konkuk.ac.kr/synteny_portal/

R Shiny in Life Sciences – Top 7 Dashboard Examples

Neel — Fri, 01 Apr 2022 19:05:03 -0500

R Shiny is one of the easiest ways for developers to make production-ready dashboards when speed and functionality are crucial. Shiny is approachable with a lot of documentation available, and because of this, a lot of developers/researchers with non-coding backgrounds are able to produce some impressive results. The whole ecosystem is easy to get your head around and pretty much limitless with regard to what you can do.

Address of the bookmark: https://www.r-bloggers.com/2022/03/r-shiny-in-life-sciences-top-7-dashboard-examples/

fqtools

Jit — Thu, 08 Dec 2016 09:31:12 -0600

fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are supported. See below for a full list of the subcommands available and a brief description of their purpose. Most of the individual subcommands will take either a single file or a pair of files as input. If no input file is specified, fqtools will attempt to read data from stdin. In this case, it is advisabe to specify the format of the data provided. For subcommands that generate FASTQ data, either a single file or a pair of files will be generated. If no -o argument is provided, single files will be writted to stdout.

Address of the bookmark: https://github.com/alastair-droop/fqtools

Fastq format

Jit — Wed, 03 May 2017 04:23:32 -0500

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer.^[1]

Address of the bookmark: https://en.wikipedia.org/wiki/FASTQ_format

IPython: Interactive notebooks

Rahul Nayak — Fri, 07 Nov 2014 12:07:02 -0600

The IPython Notebook is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document.

These notebooks are normal files that can be shared with colleagues, converted to other formats such as HTML or PDF, etc. You can share any publicly available notebook by using the IPython Notebook Viewer service which will render it as a static web page. This makes it easy to give your colleagues a document they can read immediately without having to install anything.

To learn more about using the IPython Notebook, you can visit our example collection, and you can read the documentation for all the details on how to use and configure the system. The Notebook Gallery showcases many interesting notebooks covering a variety of topics, from basic programming to advanced scientific computing.

More http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261

http://ipython.org/ipython-doc/1/interactive/notebook.html

Reference http://ipython.org/notebook.html

iTOL: Interactive Tree Of Life

Rahul Nayak — Tue, 18 Jul 2017 05:36:51 -0500

Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic trees.

Explore your trees directly in the browser, and annotate them with various types of data.

iTOL can easily visualize trees with 50'000 or more leaves. With advanced search capabilities and display of unrooted, circular and regular cladograms or phylograms, exploring and navigating trees of any size is simple.

https://itol.embl.de/

Address of the bookmark: https://itol.embl.de/

chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes

Neel — Fri, 12 Apr 2019 05:30:41 -0500

Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.

Address of the bookmark: https://cran.r-project.org/web/packages/chromoMap/vignettes/chromoMap.html