BOL: Related items

R package for visualising GO enrichment

Jit — Mon, 22 Jul 2013 12:25:09 -0500

An R package that visualizes the GO enrichment results as word clouds and arranges them together with figures of experimental data. This allows us to draw informative summary plots for analyses such as differential expression or clustering, where for each gene list we display its behaviour in the experiment alongside with its GO annotations.

Links @ http://raivokolde.github.io/GOsummaries/

Lab @ http://biit.cs.ut.ee/about/main

JRF Bioinformatics at National Chemical Laboratory

Sun, 03 Jan 2016 05:59:05 -0600

Junior Project Fellow Bioinformatics
Eligibility : ME/M.Tech, MSc(Bio-Informatics)
Location : Pune
Last Date : 08 Jan 2016
Hiring Process : Written-test, Face to Face Interview
National Chemical Laboratory

Junior Project Fellow Jobs opportunity in National Chemical Laboratory on contract basis
Project Code : BSC0117
Title of the Project : Plant?Microbe and Soil Interactions (PMSI)
No. of Post : 01
Qualification : M.Tech. / M.Sc. in Bioinformatics from a recognized university with minimum of 55% marks (aggregate) and sound Bioinformatics knowledge / experience
Desirable : Good knowledge of Linux (command line and GUI) and SQL; Java / Perl / Python / R / Bash programing / scripting; Analysis of NGS data; Protein modeling / docking; Development and maintenance of web & database servers, etc
Emoluments : Rs. 16,000/?
Age Limit : 28 Years
Selection Procedure : Written Test / Interview
How to apply
Applications neatly typed in the prescribed proforma (enclosed herewith) duly completed and signed together with photo?copies of relevant certificates/ testimonials and photograph should be addressed to : The Head, Biochemical Sciences Division, Attn : Dr. Narendra Kadoo, CSIR?National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411 008, so as to reach on or before 08/01/2016. Please superscribe the envelop “Application for Junior Project Fellow (Project: BSC0117)”.

More at http://www.ncl-india.org/files/JoinUs/JobVacancies/TemporaryJobs.aspx?

Surrogate Variable Analysis (SVA)

Jit — Thu, 30 Oct 2014 08:01:58 -0500

The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways:

(1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS),

(2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and

(3) removing batch effects with known control probes (Leek 2014 biorXiv).

Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).

More at http://www.bioconductor.org/packages/release/bioc/html/sva.html

JRF Bioinformatics at CUK

Thu, 03 Dec 2015 23:40:38 -0600

JRF Bioinformatics

Eligibility : MSc(Bio-Informatics), BE/B.Tech

Location : Kasaragod

Last Date : 20 Dec 2015

Hiring Process : Face to Face Interview
Central University of Kerala

JRF job opportunity in Central University of Kerala (CUK) on temporary basis

Project Title : "Targeting TAL effector mediated susceptibility for durable and broad-spectrum resistance to bacterial blight in Rice"

No. of Post : 01

Qualification : MSc in any subject under Life Science or Bioinformatics/ B.Tech in Bioinformatics + 1 yr experience

Stipend : Rs. 14,000/-
How to apply

Interested candidates are requested to send their applications explaining their interest in the position with an updated CV to Dr. Ginny Antony, Assistant Professor, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Padannakkad, Kasaragod, Kerala - 671 314 email: ginnycuk2013@gmail.com on or before 20th December, 2015.

Circular plots in R

Jit — Mon, 19 Jun 2017 06:20:27 -0500

Circular plots are useful to represent complicated informations. They are used in 2 specific cases: when you have long axis and numerous categories, and when you want to show relationships between elements. The circos gallery displays several examples of circular plots, what gives a nice overview of the possibilities. Circos is the most famous

tool to create circular plots. Thanks to Zuguang Gu, the Circlize library makes the circos functions available in R! It implements low-level graphic functions for adding common graphics in a circular layout. This page aims to learn you how to use the library, so I strongly advise to read the graphics in the proposed order!

http://www.r-graph-gallery.com/portfolio/circular-plot/

Address of the bookmark: http://www.r-graph-gallery.com/portfolio/circular-plot/

JRF/Traineeship/Studentship Bioinformatics

Thu, 10 Dec 2015 13:49:56 -0600

JRF/Traineeship/Studentship Bioinformatics

Eligibility : ME/M.Tech(Bio-Informatics/Bio-Chemistry Engg, CSE), MSc(Bio-Informatics, CS)

Location : Delhi

Last Date : 18 Dec 2015

Hiring Process : Walk - In
IARI - Job Details

JRF/Traineeship/Studentship Bioinformatics job position in Indian Agricultural Research Institute (IARI) purely temporary

JRF

Qualification: i) Master’s degree in Bioinformatics or Computer Science + NET qualification, or ii) M. Tech degree in Bioinformatics or Computer Science/Engineering

Desirable: Efficiency to handle agricultural databases and bioinformatics tool development

Pay Scale :Rs 25000/-

Age limit : 35 years

Traineeship/2 Post

Qualification: M.Sc./M. Tech (Bioinformatics) with 60 % marks from a recognized University

Pay Scale :Rs. 8000/-consolidated

Age limit : 35 years

Studentship/4 Post

Qualification: Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University

Pay Scale :Rs. 8000/-consolidated

Age limit : 35 years
How to apply

Walk-in-Interview will be held on 18th December 2015 at 10:00 AM at AKMU, LBS Building,IARI, Pusa Campus, New Delhi-110012. Bring self attested copies and originals of all certificates ( class 10th )onwards along with biodata in the attached format, proof of date of birth, one passport size photo, NOC from present employer, if any.

More at http://www.iari.res.in/index.php?option=com_jumi&fileid=24&Itemid=664

IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer

Jit — Thu, 23 Nov 2017 10:24:19 -0600

This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It includes a functions to generate a number plots for examining the statistics that we think will be useful for this task.

However, nanopore sequencing is an emerging and rapidly developing technology. It is not clear what will be most informative. We hope that IONiseR will provide a framework for visualisation of metrics that we haven’t thought of, and welcome feedback at mike.smith@embl.de.

If you’re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final section of this document.

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

JRF Bioinformatics job position in University of Hyderabad

Tue, 29 Dec 2015 01:00:18 -0600

JRF Bioinformatics

Eligibility : ME/M.Tech(Bio-Informatics/Bio-Chemistry Engg), MSc(Bio-Informatics)

Location : Hyderabad

Last Date : 30 Dec 2015

Hiring Process : Written-test
University of Hyderabad

JRF Bioinformatics job position in University of Hyderabad

Project Entitled : Programming protective humoral responses with novel vaccine formulations against Dengue Virus

Essential Qualifications : M. Sc. in Life Sciences/Bioinformatics/ or M. Tech in Bioinformatics with a minimum of 60% marks and with CSIR-UGC JRF/NET or valid GATE score are preferred. Desirable : Candidates should have six months to one year hands on experience in molecular biology techniques like gene cloning, protein expression and purification, hands on various nano-formulations for drug/vaccine delivery, immunological assays including animal handling, immunizations, T cells and B cell assays or Candidate should have strong background in Bioinformatics and computational Biology, good programming skill particularly proficiency in R/PERL/PYTHON. Candidates interested in above position should send a one page statement clearly explaining how their skills are relevant to the above said position. The candidates should also enclose detailed CV and the name/Email IDs of three references

Fellowship : Rs. 16,000 p.m. + 30% H.R.A. for the first two years (Revised DBT fellowship guidelines maybe applicable)

Duration : The appointment will be on temporary basis for a period of one year. Based on performance, the appointment could be extended till the end of project

How to apply

Submit your application (hardcopy) in a closed envelope to Dr.Nooruddin
Khan, Room S-66B,Department of Biotechnology and Bioinfromatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046 or E mail: nklabsls@gmail.com. Last date for receipt of applications is on or before 30.12.2015

More at http://uohyd.ac.in/index.php/component/content/article/87-administration/recruitments/129

R 3.5.0 has been Released!

Jit — Thu, 26 Apr 2018 11:31:58 -0500

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

Hoffman Lab

Tue, 12 Jan 2016 02:47:41 -0600

They develop machine learning techniques to better understand chromatin biology. These models and algorithms transform high-dimensional functional genomics data into interpretable patterns and lead to new biological insight.

https://www.pmgenomics.ca/hoffmanlab/