<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38067?offset=180 https://bioinformaticsonline.com/news/view/40085/github-replacement Thu, 26 Sep 2019 03:42:39 -0500 https://bioinformaticsonline.com/news/view/40085/github-replacement <![CDATA[Github replacement !]]> For a number of reasons researchers have been trying out GitLab as a replacement for for both GitHub and various continuous integration systems, and have been exploring configurations useful for model-fitting pipelines. Researchers turned one of these into an example repository that shows how to use GitLab together with the Rocker Docker images and the drake build system to reproducibly run a project pipeline, using the cacheing functionality across all three tools to make things reasonably speedy and enable both local and remote builds.

Check it out at https://gitlab.com/ecohealthalliance/drake-gitlab-docker-example.

]]> Rahul Nayak https://bioinformaticsonline.com/opportunity/view/40770/scientist-bioinformatics-positions Thu, 30 Jan 2020 06:53:40 -0600 <![CDATA[Scientist Bioinformatics Positions]]> Bioinformatics-Multi_Omics_Integration

https://www.researchgate.net/job/939073_Senior_Scientist_Bioinformatics-Multi_Omics_Integration


Senior_Scientist_Bioinformatics-Transcriptomics_Analysis

https://www.researchgate.net/job/939075_Senior_Scientist_Bioinformatics-Transcriptomics_Analysis-Belgium_France_Switzerland_The_Netherlands

Senior Scientist Bioinformatics - Network Analytics

https://www.researchgate.net/job/939070_Senior_Scientist_Bioinformatics-Network_Analytics_Belgium_France_Switzerland_the_Netherlands

Team Leader Bioinformatics Data Sciences - Mechelen, Belgium

https://www.researchgate.net/job/938787_Team_Leader_Bioinformatics_Data_Sciences-Mechelen_Belgium

]]> https://bioinformaticsonline.com/bookmarks/view/41272/rainbowr-reliable-association-inference-by-optimizing-weights-with-r-r-package-for-snp-set-gwas-and-multi-kernel-mixed-model Fri, 28 Feb 2020 23:27:37 -0600 https://bioinformaticsonline.com/bookmarks/view/41272/rainbowr-reliable-association-inference-by-optimizing-weights-with-r-r-package-for-snp-set-gwas-and-multi-kernel-mixed-model <![CDATA[RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS and multi-kernel mixed model)]]> RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows.

  • Single-SNP GWAS with RGWAS.normal function
  • SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests multiple SNPs at the same time)
  • Check epistatic (SNP-set x SNP-set interaction) effects with RGWAS.epistasis (very slow and less reliable)

https://github.com/KosukeHamazaki/RAINBOWR

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007663

https://cran.r-project.org/web/packages/RAINBOWR/index.html

Address of the bookmark: https://github.com/KosukeHamazaki/RAINBOWR

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/42299/platypus-%E2%80%93-r-package-for-object-detection-and-image-segmentation Mon, 09 Nov 2020 02:56:25 -0600 https://bioinformaticsonline.com/bookmarks/view/42299/platypus-%E2%80%93-r-package-for-object-detection-and-image-segmentation <![CDATA[Platypus – R package for object detection and image segmentation.]]> platypus is an R package for object detection and semantic segmentation. Currently using 

platypus you can perform:
  • multi-class semantic segmentation using U-Net architecture
  • multi-class object detection using YOLOv3 architecture

You can install the latest version of platypus with remotes package:

remotes::install_github("maju116/platypus")

Note that in order to install platypus you need to install keras and tensorflow packages and Tensorflow version >= 2.0.0 ( Tensorflow 1.x will not be supported!)

Address of the bookmark: https://github.com/maju116/platypus

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43848/r-shiny-in-life-sciences-%E2%80%93-top-7-dashboard-examples Fri, 01 Apr 2022 19:05:03 -0500 https://bioinformaticsonline.com/bookmarks/view/43848/r-shiny-in-life-sciences-%E2%80%93-top-7-dashboard-examples <![CDATA[R Shiny in Life Sciences – Top 7 Dashboard Examples]]>  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/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44487/r-package-for-pca-analysis Sun, 24 Mar 2024 20:06:24 -0500 https://bioinformaticsonline.com/bookmarks/view/44487/r-package-for-pca-analysis <![CDATA[R Package for PCA Analysis]]> An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on GitHub: https://github.com/Devashish13/PopulationStructure

Address of the bookmark: https://rpubs.com/Devashish13/PCAGenomics

]]> LEGE https://bioinformaticsonline.com/blog/view/41455/coronavirus-covid-%E2%80%9019-testing-sites-in-india Mon, 16 Mar 2020 16:13:41 -0500 https://bioinformaticsonline.com/blog/view/41455/coronavirus-covid-%E2%80%9019-testing-sites-in-india <![CDATA[Coronavirus COVID ‐19 Testing Sites In India]]> COVID-19 is a new illness that can affect your lungs and airways. It's caused by a virus called coronavirus.

Stay at home if you have coronavirus symptoms

Stay at home if you have either:

  • a high temperature – you feel hot to touch on your chest or back
  • a new, continuous cough – this means you've started coughing repeatedly

DO NOT TAKE

Ibrufen

https://amp.theguardian.com/world/2020/mar/14/anti-inflammatory-drugs-may-aggravate-coronavirus-infection

How to avoid catching and spreading coronavirus (social distancing)

Everyone should do what they can to stop coronavirus spreading.

It is particularly important for people who:

  • are 70 or over
  • have a long-term condition
  • are pregnant
  • have a weakened immune system

image

Below are the 52 Coronavirus COVID-19 Testing sites/locations in India.

State: Andhra Pradesh       

  1. Sri Venkateswara Institute of Medical Sciences, Tirupati
  2. Andhra Medical College, Visakhapatnam, Andhra Pradesh
  3. GMC, Anantapur, AP

State: Andaman & Nicobar islands

  1. Regional Medical Research Centre, Port Blair, Andaman, and Nicobar

State: Assam

  1. Gauhati Medical College, Guwahati
  2.  Regional Medical Research Center, Dibrugarh

State: Bihar

  1. Rajendra Memorial Research Institute of Medical Sciences, Patna

State: Chandigarh

  1. Post Graduate Institute of Medical Education & Research, Chandigarh

State: Chhattisgarh

  1. All India Institute Medical Sciences, Raipur

Union Territory: Delhi-NCT 

  1. All India Institute Medical Sciences, Delhi
  2. National Centre for Disease Control, Delhi

State: Gujarat

  1. BJ Medical College, Ahmedabad
  2. M.P.Shah Government Medical College, Jamnagar

State: Haryana

  1. Pt. B.D. Sharma Post Graduate Inst. of Med. Sciences, Rohtak, Haryana
  2. BPS Govt Medical College, Sonipat

State: Himachal Pradesh

  1. Indira Gandhi Medical College, Shimla, Himachal Pradesh
  2. Dr.Rajendra Prasad Govt. Med. College, Kangra, Tanda, HP

Union Territory: Jammu and Kashmir

  1. Sher‐e‐ Kashmir Institute of Medical Sciences, Srinagar
  2. Government Medical College, Jammu

State: Jharkhand

  1. MGM Medical College, Jamshedpur

State: Karnataka

  1. Bangalore Medical College & Research Institute, Bangalore
  2. National Institute of Virology Field Unit Bangalore
  3. Mysore Medical College & Research Institute, Mysore
  4. Hassan Inst. of Med. Sciences, Hassan, Karnataka
  5. Shimoga Inst. of Med. Sciences, Shivamogga, Karnataka

State: Kerala

  1. National Institute of Virology Field Unit, Kerala
  2. Govt. Medical College, Thiruvananthapuram, Kerala
  3. Govt. Medical College, Kozhikode, Kerala

State: Madhya Pradesh

  1. All India Institute Medical Sciences, Bhopal
  2. National Institute of Research in Tribal Health (NIRTH), Jabalpur

State: Meghalaya

  1. NEIGRI of Health and Medical Sciences, Shillong, Meghalaya

State: Maharashtra

  1. Indira Gandhi Government Medical College, Nagpur
  2. Kasturba Hospital for Infectious Diseases, Mumbai

State: Manipur

  1. J N Inst. of Med. Sciences Hospital, Imphal‐East, Manipur

State: Odisha

  1. Regional Medical Research Center, Bhubaneswar

Union Territory: Puducherry

  1. Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry

State: Punjab

  1. Government Medical College, Patiala, Punjab
  2. Government Medical College, Amritsar

State: Rajasthan

  1. Sawai Man Singh, Jaipur
  2. Dr. S.N Medical College, Jodhpur
  3. Jhalawar Medical College, Jhalawar, Rajasthan
  4. SP Med. College, Bikaner, Rajasthan

State: Tamil Nadu

  1. King’s Institute of Preventive Medicine & Research, Chennai
  2. Government Medical College, Theni

State: Tripura

  1. Government Medical College, Agartala

State: Telangana

  1. Gandhi Medical College, Secunderabad

State: Uttar Pradesh

  1. King’s George Medical University, Lucknow
  2. Institute of Medical Sciences, Banaras, Hindu University, Varanasi
  3. Jawaharlal Nehru Medical College, Aligarh

State: Uttarakhand

  1. Government Medical College, Haldwani

State: West Bengal

  1. National Institute of Cholera and Enteric Diseases, Kolkata
  2. IPGMER, Kolkata
]]> Neel https://bioinformaticsonline.com/bookmarks/view/42357/irscope-an-online-program-to-visualize-the-junction-sites-of-chloroplast-genomes Wed, 25 Nov 2020 19:44:46 -0600 https://bioinformaticsonline.com/bookmarks/view/42357/irscope-an-online-program-to-visualize-the-junction-sites-of-chloroplast-genomes <![CDATA[IRscope: an online program to visualize the junction sites of chloroplast genomes]]> eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.

Address of the bookmark: https://sites.google.com/g.hmc.edu/empress/home

]]> Neel https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter Fri, 12 Oct 2018 04:37:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter <![CDATA[DNA Nucleotide Counter]]> DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity Wed, 12 Dec 2018 08:36:08 -0600 https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity <![CDATA[OrthoANI: An improved algorithm and software for calculating average nucleotide identity]]> OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be integrated into preexisting bioinformatics pipelines. 

Address of the bookmark: https://www.ezbiocloud.net/tools/orthoani

]]> Abhimanyu Singh