<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37674?offset=290 https://bioinformaticsonline.com/bookmarks/view/36109/sankeynetwork-with-networkd3 Fri, 06 Apr 2018 12:07:55 -0500 https://bioinformaticsonline.com/bookmarks/view/36109/sankeynetwork-with-networkd3 <![CDATA[sankeyNetwork with networkD3]]> You can also create Sankey diagrams with sankeyNetwork. Here is an example using downloaded JSON data:

https://en.wikipedia.org/wiki/Sankey_diagram

Address of the bookmark: https://christophergandrud.github.io/networkD3/#sankey

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39039/dotplotly-generate-an-interactive-dot-plot-from-mummer-or-minimap-alignments Thu, 21 Feb 2019 10:22:17 -0600 https://bioinformaticsonline.com/bookmarks/view/39039/dotplotly-generate-an-interactive-dot-plot-from-mummer-or-minimap-alignments <![CDATA[dotPlotly: Generate an interactive dot plot from mummer or minimap alignments]]> Create an interactive dot plot from mummer output OR PAF format

R script that makes a plotly interactive and/or static (png/pdf) dot plot.

Shiny app available for testing

Address of the bookmark: https://github.com/tpoorten/dotPlotly

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools Thu, 17 Feb 2022 05:37:55 -0600 https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools <![CDATA[Comparative genomics visualisation tools !]]> Comparative genomics visualisation tools !

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

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44362/biostats-book Mon, 14 Aug 2023 03:11:39 -0500 https://bioinformaticsonline.com/bookmarks/view/44362/biostats-book <![CDATA[Biostats book !]]> https://practical-stats-med-r.netlify.app/

Address of the bookmark: https://practical-stats-med-r.netlify.app/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/4099/sequencing-solutions-to-world-health Thu, 29 Aug 2013 15:05:35 -0500 https://bioinformaticsonline.com/bookmarks/view/4099/sequencing-solutions-to-world-health <![CDATA[Sequencing Solutions to World Health]]> "New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine."

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/2726/comparison-of-short-read-de-novo-alignment-algorithms Wed, 21 Aug 2013 07:56:01 -0500 https://bioinformaticsonline.com/bookmarks/view/2726/comparison-of-short-read-de-novo-alignment-algorithms <![CDATA[Comparison of Short Read De Novo Alignment Algorithms]]> Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references.

Title: Comparison of Short Read De Novo Alignment Algorithms 

Author: Nikhil Gopal

Address of the bookmark: http://biochem218.stanford.edu/Projects%202011/Gopal%202011.pdf

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/4208/latest-paper-on-comparison-of-mapping-tools Tue, 03 Sep 2013 18:00:38 -0500 https://bioinformaticsonline.com/bookmarks/view/4208/latest-paper-on-comparison-of-mapping-tools <![CDATA[Latest paper on comparison of mapping tools]]> A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013.

http://bmi.osu.edu/hpc/software/benchmark/

http://bmi.osu.edu/hpc/software/pmap/pmap.html

Other similiar papers:

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022

http://bioinformatics.oxfordjournals.org/content/28/24/3169

Some new Mapping tool links:

GSNAP

http://research-pub.gene.com/gmap/

RMAP

http://rulai.cshl.edu/rmap/

mrsFAST

http://mrsfast.sourceforge.net/Home

http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/

BFAST

http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page

SHRiMP (for AB SOLiD color-space reads)

http://compbio.cs.toronto.edu/shrimp/

RazerA 3

http://www.seqan.de/projects/razers/

Address of the bookmark: http://www.biomedcentral.com/1471-2105/14/184

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/9400/largest-genome-sequenced Fri, 21 Mar 2014 13:57:19 -0500 https://bioinformaticsonline.com/bookmarks/view/9400/largest-genome-sequenced <![CDATA[Largest Genome Sequenced]]> The enormous size of the loblolly pine genome having 22 billion base pairs compared to only 3 billion in the human genome. In other words, it is seven times larger than a human’s and also the largest and the most complete conifer genome ever sequenced.

Related Paper:

http://genomebiology.com/2014/15/3/R59/abstract

 

Address of the bookmark: http://www.news.ucdavis.edu/search/news_detail.lasso?id=10859

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool Fri, 25 Apr 2014 10:59:04 -0500 https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool <![CDATA[New RNA Seq tool]]> "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy."

Tool link:

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Address of the bookmark: http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/

]]> Rahul Agarwal https://bioinformaticsonline.com/news/view/10966/genxpro-gmbh Thu, 22 May 2014 07:18:35 -0500 https://bioinformaticsonline.com/news/view/10966/genxpro-gmbh <![CDATA[GenXPro GmbH]]> GenXPro GMbH is service provider for entire spectrum of nucleotide-based information of any biological sample. By combining intelligent data reduction techniques and latest next generation sequencing technologies, our service portfolio provides most accurate and cost efficient solutions for transcriptomic-, genomic- or epigenomic research.

GENXPRO GMBH, ALTENHÖFERALLEE 3, 60438 FRANKFURT MAIN, GERMANY

Website: http://www.genxpro.info/products_and_services/

PHONE: +49 (0)69- 95 73 97 10, FAX: +49 (0)69- 95 73 97 06

EMAIL: info@genxpro.de

]]> Rahul Agarwal