BOL: Related items

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

dcGOR

Martin Jones — Sat, 08 Nov 2014 14:54:28 -0600

An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929). The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR), and also at GitHub for version control.

The dedicated website is available in http://supfam.org/dcGOR, from which several demos are also provided:

1. Analysing SCOP domains: http://supfam.org/dcGOR/demo-Fang.html

2. Analysing Pfam domains: http://supfam.org/dcGOR/demo-Basu.html

3. Analysing InterPro domains: http://supfam.org/dcGOR/demo-Customisation.html

Venn Diagrams on R Studio

Jitendra Prajapati — Mon, 25 Apr 2016 16:22:28 -0500

First step: Install & load “VennDiagram” package.

# install.packages('VennDiagram')
library(VennDiagram)

Second step: Load data

Add filepath if “catdoge.csv” is not in working-directory.

d <- read.csv("catdoge.csv")

Address of the bookmark: http://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html

Enrichr: a comprehensive gene set enrichment analysis

Jit — Thu, 27 Apr 2017 05:42:09 -0500

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377

Address of the bookmark: http://amp.pharm.mssm.edu/Enrichr/

Painless package development for R

Abhi — Tue, 03 May 2016 05:31:06 -0500

Devtools makes package development a breeze: it works with R’s existing conventions for code structure, adding efficient tools to support the cycle of package development. With devtools, developing a package becomes so easy that it will be your default layout whenever you’re writing a significant amount of code.

Before you get started be sure to check out:

Address of the bookmark: https://www.rstudio.com/products/rpackages/devtools/

Pacman

Rahul Nayak — Mon, 16 Feb 2015 12:15:17 -0600

The pacman package is an R package management tool that combines the functionality of base library related functions into intuitively named functions. This package is ideally added to .Rprofile to increase workflow by reducing time recalling obscurely named functions, reducing code and integrating functionality of base functions to simultaneously perform multiple actions.

Function names in the pacman package follow the format of p_xxx where ‘xxx’ is the task the function performs. For instance the p_load function allows the user to load one or more packages as a more generic substitute for the library or require functions and if the package isn’t available locally it will install it for you.

Installation

To download the development version of pacman:

Download the zip ball or tar ball, decompress and run R CMD INSTALL on it, or use the devtools package to install the development version:

## Make sure your current packages are up to date
update.packages()
## devtools is required
devtools::install_github("trinker/pacman")

Note: Windows users need Rtools and devtools to install this way.

More at https://github.com/trinker/pacman

Post Doc Computational Biology, Bioinformatics - Network Biology & Data Science, NGS (m/f/d)

Sat, 15 Feb 2020 06:13:35 -0600

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/forschung-entwicklung/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-129867.html?suid=e522e9793b41817e52ac58d6963b94e2519920df

Requirements
Doctoral degree in Bioinformatics, Computational Biology, (Bio)physics/-mathematics, Biochemistry/Biology or similar with strong quantitative and numeric focus
Ability to numerically process complex and large data sets
Good programming skills (R/Bioconductor and/or Python preferred, Linux is a plus)
Experience in analyzing next-generation sequencing data sets using network biology
Scientific publication record in applied bioinformatics
Familiarity with single cell NGS analyses and other –omics techniques is a plus, but not essential

scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

Jit — Fri, 02 Mar 2018 04:29:47 -0600

scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.

Address of the bookmark: http://scikit-bio.org/

Multiple PhD positions

Sun, 09 Feb 2020 03:10:28 -0600

14 PhD positions in the EU Horizon 2020 Marie Skłodowska-Curie Project PRECODE:
International training network which sets a joint research programme to train a new generation of leading scientists in model systems and methods for the development of new therapies for pancreatic cancer (PaCa)

http://precode-project.eu/jobs-board/#1572451761376-39d75f63-c6fb

Science for Life Laboratory (SciLifeLab)-Sweden

Sat, 10 May 2014 06:22:30 -0500

Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.

Webpage : https://www.scilifelab.se/about-us/
Opportunity: https://www.scilifelab.se/about-us/career/