BOL: Related items

Internship program with ArrayGen Technolgies

Sun, 22 Jun 2014 23:18:31 -0500

Internship Program for Bioinformatics / Biotechnology Professionals Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

Interested candidates may email their resume along with a cover letter to careers@arraygen.com

Official website: http://www.arraygen.com/

MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites

Neel — Mon, 05 Nov 2018 08:12:45 -0600

An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Address of the bookmark: https://github.com/olarerin/metaPlotR

genoPlotR - plot gene and genome maps project!

Abhimanyu Singh — Wed, 12 Dec 2018 08:33:41 -0600

genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files.

Features

Linear representation of several segments of DNA
Comparisons represented by areas between the segments (like Artemis, for example)
Reads from common formats: Genbank, EMBL, blast, Mauve, and from user-generated tab files
Plot several subsegments of the same segment on the same line, separated by a //
Automatic or manual placement of the segments on the plot
Add annotations to all the lines
Create smart, automatic annotations for genomes, based on gene names
Add a user-generated tree
Add a global scale or a scale to each line
Use user-defined graphical functions to represent genes

Address of the bookmark: http://genoplotr.r-forge.r-project.org/

chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes

Jit — Sat, 07 Sep 2019 10:45:31 -0500

chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc.) on the chromosome plot.Each chromosome is composed of loci(representing a specific range determined based on chromosome length) that, on hover, shows details about the annotations in that locus range. The plots can be saved as HTML documents that can be shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

Some of the prominent features of the package are:

visualizing polyploidy simultaneously on the same plot.
annotating groups of elements as distinct colors.
creating chromosome heatmaps.
adjusting chromosome range or visualizing chromosome regions such as genes
adding labels to the plot
adding hyperlinks to each element

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

The 8000 years old Tibetian gene mutation !!!

Neel — Wed, 20 Aug 2014 21:57:44 -0500

A new study has provided insight into how gene mutation around 8,000 years ago helped Tibetans' to survive in the thin air on the Tibetan Plateau, where an average elevation is of 14,800 feet.

A study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen conditions.

About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.

In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.

Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html

Github replacement !

Rahul Nayak — Thu, 26 Sep 2019 03:42:39 -0500

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.

Scientist Bioinformatics Positions

Thu, 30 Jan 2020 06:53:40 -0600

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

RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS and multi-kernel mixed model)

Surabhi Chaudhary — Fri, 28 Feb 2020 23:27:37 -0600

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

Platypus – R package for object detection and image segmentation.

BioStar — Mon, 09 Nov 2020 02:56:25 -0600

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

R Shiny in Life Sciences – Top 7 Dashboard Examples

Neel — Fri, 01 Apr 2022 19:05:03 -0500

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/