<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42155?offset=50 https://bioinformaticsonline.com/news/view/20439/interactive-market-intelligence Mon, 19 Jan 2015 08:20:38 -0600 https://bioinformaticsonline.com/news/view/20439/interactive-market-intelligence <![CDATA[Interactive Market Intelligence]]> BioInformatics LLC, a premier research and advisory firm serving the life science industry, has launched groundbreaking, dynamic-data presentation platform, Interactive Market Intelligence— the only cloud-based market research analytics tool for the life science tools industry.

Superior to traditional PDF and PowerPoint reports, Interactive Market Intelligence allows end-users to filter, create and export literally thousands of views of data — all easily obtainable from a set of core metrics that include market, brand, customer and workflow analytics in well-defined segments of the life science market.

The Market for Real-Time PCR is the first in a series of topics to be explored using the Interactive Market Intelligence platform. The primary research analysis is based on a survey of 900+ international scientists performing qPCR in their laboratories.

Key data findings from "The Market for Real-Time PCR": Global market for qPCR in 2015 is estimated to be $3.6B; The average growth in qPCR throughput is expected to be at 9.8% in 2015; 22% of respondents are highly likely to switch primary suppliers of qPCR products; 50% of respondents use pre-designed primer/probe sets.

]]> Pranjali Yadav https://bioinformaticsonline.com/bookmarks/view/39917/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes Sat, 07 Sep 2019 10:45:31 -0500 https://bioinformaticsonline.com/bookmarks/view/39917/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes <![CDATA[chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes]]> chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc.) on the chromosome plot.Each chromosome is composed of loci(representing a specific range determined based on chromosome length) that, on hover, shows details about the annotations in that locus range. The plots can be saved as HTML documents that can be shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

Some of the prominent features of the package are:

  • visualizing polyploidy simultaneously on the same plot.
  • annotating groups of elements as distinct colors.
  • creating chromosome heatmaps.
  • adjusting chromosome range or visualizing chromosome regions such as genes
  • adding labels to the plot
  • adding hyperlinks to each element

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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35135/alitv%E2%80%94interactive-visualization-of-whole-genome-comparisons Wed, 10 Jan 2018 07:08:17 -0600 https://bioinformaticsonline.com/bookmarks/view/35135/alitv%E2%80%94interactive-visualization-of-whole-genome-comparisons <![CDATA[AliTV—interactive visualization of whole genome comparisons]]> AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV

https://alitvteam.github.io/AliTV/

Address of the bookmark: https://github.com/AliTVTeam/AliTV

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system Fri, 04 Jan 2019 13:35:26 -0600 https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system <![CDATA[ZENBU: a collaborative, omics data integration and interactive visualization system]]> ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files. 
Please check our documentation wiki for details on how to use the system, or check out some of the views above.

Address of the bookmark: http://fantom.gsc.riken.jp/zenbu/

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/40969/leaflet-javascript-libraries-for-interactive-maps Mon, 10 Feb 2020 01:35:07 -0600 https://bioinformaticsonline.com/bookmarks/view/40969/leaflet-javascript-libraries-for-interactive-maps <![CDATA[Leaflet: JavaScript libraries for interactive maps]]> Leaflet is one of the most popular open-source JavaScript libraries for interactive maps.

Features

  • Interactive panning/zooming
  • Compose maps using arbitrary combinations of:
    • Map tiles
    • Markers
    • Polygons
    • Lines
    • Popups
    • GeoJSON
  • Create maps right from the R console or RStudio
  • Embed maps in knitr/R Markdown documents and Shiny apps
  • Easily render spatial objects from the sp or sf packages, or data frames with latitude/longitude columns
  • Use map bounds and mouse events to drive Shiny logic
  • Display maps in non spherical mercator projections
  • Augment map features using chosen plugins from leaflet plugins repository

https://rstudio.github.io/leaflet/

Address of the bookmark: https://rstudio.github.io/leaflet/

]]> Jit https://bioinformaticsonline.com/file/view/27455/blosum50-matrix Sat, 21 May 2016 22:12:15 -0500 https://bioinformaticsonline.com/file/view/27455/blosum50-matrix <![CDATA[BLOSUM50 Matrix]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/27110/easyfig Fri, 29 Apr 2016 05:49:39 -0500 https://bioinformaticsonline.com/bookmarks/view/27110/easyfig <![CDATA[Easyfig]]> Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig.  Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/

]]> Poonam Mahapatra https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 Thu, 12 May 2016 13:49:41 -0500 https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 <![CDATA[Release Notes for Genome Workbench 2.10.5]]> New Features in latest release

  • New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
  • New export function for BAM/cSRA coverage graphs (Tutorial)
  • New export function for alignments GFF3 format ((Tutorial))
  • Tree View: implemented new export mode based on selections (tutorial coming)
  • Tree View: added support for distance based circular trees
  • Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
  • Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)
]]> Jit https://bioinformaticsonline.com/bookmarks/view/27432/gkno Fri, 20 May 2016 18:56:37 -0500 https://bioinformaticsonline.com/bookmarks/view/27432/gkno <![CDATA[GKNO]]> gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.

http://gkno.me/how-to/install.html

http://gkno.me/software.html

Address of the bookmark: http://gkno.me/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines Wed, 15 Jun 2016 17:18:36 -0500 https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines <![CDATA[LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines]]> LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.

Publication:

  • L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.

Download:

Address of the bookmark: https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/

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