<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/29635?offset=840 https://bioinformaticsonline.com/bookmarks/view/33820/circular-visualization-in-r Wed, 05 Jul 2017 04:11:30 -0500 https://bioinformaticsonline.com/bookmarks/view/33820/circular-visualization-in-r <![CDATA[Circular Visualization in R]]> This is the documentation of the circlize package. Examples in the book are generated under version 0.4.1.

If you use circlize in your publications, I would be appreciated if you can cite:

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics. DOI: 10.1093/bioinformatics/btu393

Address of the bookmark: http://zuguang.de/circlize_book/book/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/10415/bioinformatician-stuck-in-wet-lab Tue, 06 May 2014 12:46:56 -0500 https://bioinformaticsonline.com/bookmarks/view/10415/bioinformatician-stuck-in-wet-lab <![CDATA[Bioinformatician stuck in wet-lab]]> This guide is aimed at pet bioinformaticians, and is meant to guide them towards better career development.

1. Make friends with local bioinformatics groups
2. Talk to your computing group
3. Obtain clear expectations
4. Rewrite your job description
5. Papers
6. Attend bioinformatics meetings
7. Try first, ask later

Address of the bookmark: http://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data Sun, 03 Dec 2017 15:19:18 -0600 https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data <![CDATA[MinION_GC: An R script to do some QC on MinION data]]> Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flowcell on my laptop.

https://github.com/roblanf/minion_qc

Address of the bookmark: https://github.com/roblanf/minion_qc

]]> Radha Agarkar https://bioinformaticsonline.com/news/view/36418/r-350-has-been-released Thu, 26 Apr 2018 11:31:58 -0500 https://bioinformaticsonline.com/news/view/36418/r-350-has-been-released <![CDATA[R 3.5.0 has been Released!]]>
  • The latest version of R is a major release! It comes with a ton of new features, including performance and speed improvements
  • All R packages will now be byte-compiled, hence boosting packages installed from GitHub
  • You may need to re-install all previously installed R packages; old scripts however will continue to work normally

    • More at https://cran.r-project.org/doc/manuals/r-release/NEWS.html

    ]]>     Jit     https://bioinformaticsonline.com/researchlabs/view/10739/science-for-life-laboratory-scilifelab-sweden Sat, 10 May 2014 06:22:30 -0500 <![CDATA[Science for Life Laboratory (SciLifeLab)-Sweden]]> Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.

    Webpage : https://www.scilifelab.se/about-us/
    Opportunity: https://www.scilifelab.se/about-us/career/

    ]]>         https://bioinformaticsonline.com/bookmarks/view/37732/making-2d-hilbert-curve Mon, 17 Sep 2018 05:43:35 -0500 https://bioinformaticsonline.com/bookmarks/view/37732/making-2d-hilbert-curve <![CDATA[Making 2D Hilbert Curve]]> Hilbert curve is a type of space-filling curves that folds one dimensional axis into a two dimensional space, but still keeps the locality. It has advantages to visualize data with long axis in following two aspects:

    1. greatly improve resolution of the visualization fron n to √nn;
    2. easy to visualize clusters because generally data points in the axis will also be close in the 2D space.

    This package aims to provide an easy and flexible way to visualize data through Hilbert curve. The implementation and example figures are based on following sources:

    Address of the bookmark: https://bioconductor.org/packages/devel/bioc/vignettes/HilbertCurve/inst/doc/HilbertCurve.html

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions Tue, 11 Dec 2018 08:43:51 -0600 https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions <![CDATA[regioneR: an R package for the management and comparison of genomic regions]]> Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's possible to study the association of a set of regions with other sets of regions, functions defined over the genome or essentially any user defined function.

    http://gattaca.imppc.org/regioner/

    Address of the bookmark: http://gattaca.imppc.org/regioner/

    ]]>     Jit     https://bioinformaticsonline.com/opportunity/view/11000/professorassociate-professor-assistant-professor-at-chettinad-academy-of-research-and-education Sat, 24 May 2014 00:00:15 -0500 <![CDATA[Professor/Associate Professor/ Assistant Professor at Chettinad Academy of Research and Education]]> OPEN FACULTY POSITION

    Chettinad Academy of Research and Education (CARE) invites applications from eligible and translational research-oriented candidates to the posts of Professor/Associate Professor/ Assistant Professor Computational Biology, Bioinformatics, and Pharmaceutical Chemistry.

    Emoluments: As per UGC norms (Adequate Compensation for Postdoctoral/Teaching experience)

    Candidates fulfilling the eligibility criteria as per the UGC norms can send their full CV with copies of certificates and reference letters to the following address by post or by e-mail on or before 31st May 2014

    The Registrar,
    Chettinad Academy of Research and Education,
    Chettinad Health City
    Kelambakkam, Chennai 603 103
    Tamil Nadu
    T +91 (0)44 4741 1000
    F +91 (0)44 4741 1011
    Email: jobs @chettinadhealthcity.com

    Advertisement: http://182.73.176.163/chc/ads2014.pdf

    ]]>         https://bioinformaticsonline.com/bookmarks/view/39244/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes Fri, 12 Apr 2019 05:30:41 -0500 https://bioinformaticsonline.com/bookmarks/view/39244/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes <![CDATA[chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes]]> 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

    ]]>     Neel     https://bioinformaticsonline.com/researchlabs/view/11107/the-minerva-research-group-for-bioinformatics Tue, 27 May 2014 15:48:14 -0500 <![CDATA[The Minerva Research Group for Bioinformatics]]> The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.

    http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

    Kelso Group
    Department of Evolutionary Genetics
    Max Planck Institute for Evolutionary Anthropology
    Deutscher Platz 6
    04103 Leipzig
    Germany
    Phone: +49 341 3550 500

    Job:
    http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40

    ]]>