Using RCy3 with Cytoscape: GSOC Wrap Up
This summer I had the pleasure of working with the National Resource for Network Biology (NRNB as a summer intern as part of Google Summer of Code project. For my project (described more in depth in the previous blog post) I wanted to make workflows for biologists to make their analyses more straightforward by using the programming language R with the Bioconductor package RCy3.
Extending RCy3 Vignettes (Google Summer of Code Project)
Cytoscape is a popular open-source program for visualizing and analyzing networks (biological and otherwise).
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 number of very helpful features in tools like Microsoft Powerpoint that are missing when making presentations in RStudio. A template presentation is available at this GitHub repository that has the features described in this post.
CBioPortal and cgdsr: An Introduction
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 and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications.
Pathway Commons and paxtoolsr: An Introduction
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 provide a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC).
Introduction to Statistical Methods in R
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 preparation of analysis results (including the development of visualizations to communicate findings).
Introduction to R
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 and writing data from/to files, plotting and installing R packages (and getting help for the packages.
Introduction to CellMiner and rcellminer
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 platforms for gene and protein expression, copy number, mutation, and others. The purpose of the CellMiner project has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.
Introduction to R Shiny Web Applications
Installing R and RStudio
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 overview to the R language, and they provide instructions on downloading and installing R and RStudio, as well as, showing some of the main features of RStudio.