Blog Archives

Extending RCy3 Vignettes (Google Summer of Code Project)

August 4, 2016
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Extending RCy3 Vignettes (Google Summer of Code Project)

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...

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Tips on Creating Presentations with RStudio and Webpage Embedding

August 1, 2016
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Tips on Creating Presentations with RStudio and Webpage Embedding

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 are dynamically generated when the presentation is created. There are...

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Tips on Creating Presentations with RStudio and Webpage Embedding

August 1, 2016
By
Tips on Creating Presentations with RStudio and Webpage Embedding

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 are dynamically generated when the presentation is created. There are...

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Pathway Commons and paxtoolsr: An Introduction

February 8, 2016
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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 its native BioPAX format to Read More ...The post...

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Introduction to CellMiner and rcellminer

January 18, 2016
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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 have been extensively characterized by many Read More ...The post...

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Introduction to Statistical Methods in R

January 18, 2016
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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 models, and the interpretation and Read More ...The post...

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Introduction to R Shiny Web Applications

January 18, 2016
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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 Shiny is flexible enough to Read More ...The post...

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Introduction to R

January 18, 2016
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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 data.frames. It also covers reading Read More ...The post...

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Installing to R and RStudio

January 17, 2016
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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 users. The slides below give an Read More ...The post...

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CBioPortal and cgdsr: An Introduction

January 11, 2016
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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 access to molecular profiles Read More ...The post...

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