BOL: Related items

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

Making 2D Hilbert Curve

Jit — Mon, 17 Sep 2018 05:43:35 -0500

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:

greatly improve resolution of the visualization fron n to √nn;
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

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

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

New Machine Learning Packages in R

Rahul Nayak — Fri, 27 Mar 2020 12:11:21 -0500

Machine Learning

autokeras v1.0.1: Implements an interface to AutoKeras, an open source software library for automated machine learning. See README for an example.

MTPS v0.1.9: Implements functions to predict simultaneous multiple outcomes based on revised stacking algorithms as described in Xing et al. (2019). See the vignette to get started.

quanteda.textmodels v0.9.1: Implements methods for scaling models and classifiers based on sparse matrix objects representing textual data. It includes implementations of the Laver et al. (2003) wordscores model, the Perry & Benoit’s (2017) class affinity scaling model, and the Slapin & Proksch (2008) wordfish model. See the vignette to get started.

SeqDetect v1.0.7: Implements the automaton model found in Krleža, Vrdoljak & Brčić (2019) to detect and process sequences. See the vignette for examples and theory.

studyStrap v1.0.0: Implements multi-Study Learning algorithms such as Merging, Study-Specific Ensembling (Trained-on-Observed-Studies Ensemble), the Study Strap, and the Covariate-Matched Study Strap. and offers over 20 similarity measures. See Kishida, et al. (2019) for background and the vignette for how to use the package.

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/

TGNet

Shruti Paniwala — Wed, 24 Aug 2016 05:36:36 -0500

Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis.

Visualization and quality assessment of de novo genome assemblies

Citation

This software is fully described in the paper:
Riba-Grognuz, Keller, Falquet, Xenarios & Wurm (2011) Visualization and quality assessment of de novo genome assemblies.

In brief, our scripts create Cytoscape files to visualize transcript evidence that suggests adjacency between scaffolds and contigs.

Software requirements

BLAT (tested with Standalone BLAT v. 32×1). Source Binaries .
Cytoscape (tested with versions 2.7.0, 2.8.2)
a UNIX machine (tested on Mac OS X 10.6 and CentOS 4.6)

Address of the bookmark: https://github.com/ksanao/TGNet

J-Circos

Shruti Paniwala — Fri, 17 Feb 2017 09:06:54 -0600

Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Address of the bookmark: http://www.australianprostatecentre.org/research/software/jcircos

GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Neel — Sun, 15 Mar 2020 03:41:12 -0500

GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

GSP4PDB is part of the services provided by the Bioinformatic Group of the University of Talca

http://gdblab.com/gsp4pdb/gsp4pdb2/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3352-x

Address of the bookmark: http://gdblab.com/gsp4pdb/gsp4pdb2/