August 2015

parsing BED coordinates

August 6, 2015 | R on Guangchuang Yu

In supplemental file of ChIPseeker paper. I compare distances to TSS reported by several ChIP annotation software, including ChIPseeker, ChIPpeakAnno, HOMER and PeakAnalyzer. Although I found that the chromStart positions in HOMER output have a +1 shift compare to other software, I did not realize this issue since all other software ...
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Matrix Factorization Comes in Many Flavors: Components, Clusters, Building Blocks and Ideals

August 6, 2015 | Joel Cadwell

Unsupervised learning is covered in Chapter 14 of The Elements of Statistical Learning. Here we learn about several data reduction techniques including principal component analysis (PCA), K-means clustering, nonnegative matrix factorization (NMF) and archetypal analysis (AA). Although on the surface they seem so different, each is a data approximation technique using ... [Read more...]

Authenticated API Testing Using Travis CI

August 6, 2015 | Randy Zwitch

As I’ve become more serious about contributing in the open-source community, having quality tests for my packages has been something I’ve spent much more time on than when I was just writing quick-and-dirty code for my own purposes. My most used open-sourced package is RSiteCatalyst, which accesses the ... [Read more...]

Peeling of group layers.

August 6, 2015 | Christoph Safferling

As an experienced dplyr user since almost day one, I thought I knew every aspect of it. But when my new colleague, who is learning dplyr from scratch, asked me to explain the peeling of group layers with summarise, I was like, what? Turns out this... [Read more...]

Patent Datasets

August 6, 2015 | Paul Oldham's Analytics Blog

One problem for people seeking to learn patent analytics is a lack of access to patent data from different sources. In this article I introduce the patent datasets developed for the WIPO Open Source Patent Analytics Project as training sets for patent... [Read more...]

Peeling of group layers.

August 6, 2015 | Christoph Safferling

As an experienced dplyr user since almost day one, I thought I knew every aspect of it. But when my new colleague, who is learning dplyr from scratch, asked me to explain the peeling of group layers with summarise, I was like, what? Turns out this actually is a thing. ... [Read more...]

Just another way to make a R flavored blog

August 6, 2015 | Joshua Kunst

This post is in active development! image source This usually is "echo=FALSE"
<span>rm</span><span>(</span><span>list</span> <span>=</span> <span>ls</span><span>())</span>
<span>library</span><span>(</span><span>"printr"</span><span>)</span>
knitr<span>::</span>opts_knit<span>$</span>set<span>(</span>root.dir  <span>=</span> <span>normalizePath</span><span>(</span><span>".."</span><span>))</span>
Considerations Use h2 ## in R files to spin, because h1 is reserved for title post. At the begin of R script write a chunk of R code loading the print package This post have some considerations ... [Read more...]

Compiling RMarkdown from a Helper R Script

August 6, 2015 | Stephen Turner

The problemI was looking for a way to compile an RMarkdown document and have the filename of the resulting PDF or HTML document contain the name of the input data that it processed. That is, if I compiled the analysis.Rmd file, where in that file it did some analysis ... [Read more...]

A simple statnet model of CRAN

August 6, 2015 | Joseph Rickert

by Joseph Rickert In a recent post on creating JavaScript network graphs directly from R, my colleague and fellow blogger, Andrie de Vries, included a link to a saved graph of CRAN. Here, I will use that same graph (network) to build a simple exponential random graph model using functions ... [Read more...]

Tutorial Recap: Make a Census Explorer with Shiny

August 6, 2015 | Ari Lamstein

On July 28 I had the pleasure of leading a tutorial titled Make a Census Explorer with Shiny! at the San Francisco R-ladies Meetup. A big thank you to Gabriela de Queiroz for organizing the event, Sharethrough for hosting it, and all the participants for attending. If you are interested in ...
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Simulating backgammon players’ Elo ratings

August 6, 2015 | Peter's stats stuff - R

Probabilities of winning with a given rating Backgammon clubs and on-line forums use a modified form of the Elo rating system to keep track of how well individuals have played and draw inferences about their underlying strength. The higher the rating, the stronger the player. Players with higher ratings are ... [Read more...]

Speeding Up Your Quest(s) For “R Stuff”

August 5, 2015 | hrbrmstr

I use Google quite a bit when conjuring up R projects, whether it be in a lazy pursuit of a PDF vignette or to find a package or function to fit a niche need. Inevitably, I’ll do something like this (yeah, I’m still on a mapping kick) and ...
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partools: a Sensible R Package for Large Data Sets

August 5, 2015 | matloff

As I mentioned recently, the new, greatly extended version of my partools package is now on CRAN. (The current version on CRAN is 1.1.3, whereas at the time of my previous announcement it was only 1.1.1. Note that Unix is NOT required.) It is my contention that for most R users who ... [Read more...]

Contracting and simplifying a network graph

August 5, 2015 | Andrie de Vries

by Andrie de Vries In a previous post, I used page rank and community structure to create a plot of CRAN. This plot used vibrant colours to allow us to see some of the underlying structure of CRAN. However, much of this structure was still obfuscated by the amount of ... [Read more...]

Moment conditions and Bayesian nonparametrics

August 5, 2015 | xi'an

Luke Bornn, Neil Shephard, and Reza Solgi (all from Harvard) have arXived a pretty interesting paper on simulating targets on a zero measure set. Although it is not initially presented this way, but rather in non-parametric terms as moment conditions where θ is the parameter of the sampling distribution, constrained by ...
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How to Analyze Data: 6 Useful Ways To Use Color In Graphs

August 5, 2015 | Plotly Blog

Effectively using color means your graphs clearly communicate your data. This post shows how. We summarize and apply visualization research to real-world examples. You can make graphs like these with Plotly’s web app, or APIs for Python, MATLAB, and R. For users who want to securely share graphs and ... [Read more...]
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