BOL: Related items

R tuorial

Rahul Nayak — Mon, 31 Jul 2017 08:41:40 -0500

R learning resources

https://flowingdata.com/

Address of the bookmark: https://flowingdata.com/

R googleVis examples

Rahul Nayak — Sun, 10 Dec 2017 06:13:42 -0600

It may take a little while to load all charts. Please be patient. All charts require an Internet connection.

These examples are taken from the googleVis demo. You can execute the demo via

library(googleVis)
demo(googleVis)

For more details about the charts and further examples see the helpfiles of the individual googleVis function and review the Google Charts API documentation and Terms of Service.

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

JRF/SRF at University of Hyderabad

Fri, 17 Oct 2014 01:55:44 -0500

Applications are invited for the following post of Junior Research Fellow (temporary position coterminous with the project) under DBT funded research project on ““Understanding the functions of α1β1γ1/α2β1γ1 selective AMPK Modulators in dissecting the pharmacological role of these isozymes in metabolic diseases”

Qualified and interested candidates can send their curriculum vitae by e-mail to hr@drils.org on or before 27th October 2014 mention in the subject line of the mail the following code: AMPK-Biology.

Selected candidates will be called for a personal interview to Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad. The selected candidate is expected to report within two weeks from the date of selection to start work on the project.

Junior Research Fellowship (Molecular Modeling/Biology) for two years and Senior Research fellowship for one year

Junior Research Fellowship: Rs. 15,600/- (consolidated) per month for first two years.
Senior Research Fellowship: Rs. 18,200/-(consolidated) per month for the 3rd year.

Duration: The duration of the fellowship is for three years. However, the performance of the candidate will be reviewed after the completion of every year and the fellowship will be renewed only upon satisfactory performance.

Responsibilities:

1) Literature search.
2) Design, plan and execute experiments under the supervision of the scientist.
3) Provide scientific support to the scientist in his/her research activities.
4) Book keeping and maintenance of stocks and consumables.

Essential Qualifications:

Required: M.Sc. in Microbiology/Biotechnology/Bioinformatics or any other related branch of basic Sciences from a recognized university/institute with a consistent academic record of minimum 60% aggregate in all qualifying examinations. The candidate should be NET qualified for lectureship. The candidate should be motivated to work with dedication.

Desirable: expertise/experience in both Molecular Modeling and Molecular Biology.

Experience: 0-2 years in the areas of Molecular Modeling and/or Molecular Biology and cell biology and Biochemistry.

Preferable: Relevant research experience as evident from thesis/dissertation/project work.

Advertisement: http://www.ilsresearch.org/userfiles/Junior%20REsearch%20Fellowship%20-%20AMPK(Biology).pdf

chromoMap-An R package for Interactive visualization and mapping of human chromosomes

Rahul Nayak — Mon, 25 Jun 2018 17:22:24 -0500

chromoMap is an R package that provides interactive, configurable and elegant graphics visualization of the human chromosomes 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. Because of the enormous size of the chromosomes, it is impractical to visualize each element on the same plot. But chromoMap plots provide a magnified view for each of chromosome location to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order (You will see in the demos below). Not ony that, 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.

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

visNetwork: an R package for network visualization, using vis.js javascript library

Jit — Wed, 09 Jan 2019 11:00:32 -0600

visNetwork is an R package for network visualization, using vis.js javascript library (http://visjs.org/). All remarks and bugs are welcome on github : https://github.com/datastorm-open/visNetwork.

Features

Based on htmlwidgets, so :

compatible with shiny, R Markdown documents, and RStudio viewer

The package proposes all the features available in vis.js API, and even more with special features for R :

easy to use
custom shapes, styles, colors, sizes, …
works smooth on any modern browser for up to a few thousand nodes and edges
interactivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, …)
visualize rpart tree

Address of the bookmark: https://datastorm-open.github.io/visNetwork/

GeneOverlap: An R package to test and visualize gene overlaps

Jit — Thu, 27 Dec 2018 19:45:52 -0600

Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification’s role in gene regulation.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf