Cytoscape is a popular open-source program for visualizing and analyzing networks (biological and otherwise). This summer I have been working on a Google Summer of Code project with the National Resource for Network Biology that aims to make it easier... [Read more...]

RStudio provides functionality to make presentations in R in a way very similar to knitr reports. Presentations produced in RStudio are dependent on the on reveal.js HTML presentation framework, and like knitr reports, these presentations are nice way of embedding both code chucks and have the results shown that ... [Read more...]

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Pathway Commons is an aggregation of public pathway databases and provides infrastructure for querying this rich dataset. Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC. paxtoolsr is a package that builds on the strengths of Pathway Commons and ... [Read more...]

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which ... [Read more...]

Data analyses are the product of many different tasks, and statistical methods are one key aspect of any data analysis. There is a common workflow in the related areas of informatics, data mining, data science, machine learning, and statistics. The workflow tasks include data preparation, the development of predictive mathematical ... [Read more...]

Shiny is a web framework for R developers. Shiny allows users to develop websites that help present their analyses to users by allowing the analyses to be interactive through a web-based interfaces. Shiny web-interfaces are programmed in R without the need to develop anything in HTML, CSS, or Javascript, although ... [Read more...]

R is a programming language developed by data analysts for data analysts. It offers many features that make a powerful tool for data exploration. Some basic features need to be understood to begin programming in R. The following presentation covers some of these features including working with variables, vectors and ... [Read more...]

R is a powerful language and environment for statistics and scientific graphics. Some of the main advantages of R is that is free/open-source and users can find a lot of help online. RStudio provides free interface to R that has an organized layout and many extra options for R ... [Read more...]

The cBio Cancer Genomics Portal is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 100 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality ... [Read more...]