Extending genomation to work with paired-end BAM filesExtending genomation to work with paired-end BAM filesAccelerate functions responsible for reading genomic filesParallelizing data processing in ScoreMatrixListArithmetic, indicator and logic operations as well as subsetting work on ScoreMatrix objectsImprovements and new arguments in visualization functionsFaster heatmapsNew clustering possibilities in heatmaps: “clustfun” argument ... [Read more...]

In BioC 3.2 release, all my packages including GOSemSim, clusterProfiler, DOSE, ReactomePA, and ChIPseeker switch from Sweave to R Markdown for package vignettes. GOSemSim To make it consistent between GOSemSim and clusterProfiler, 'worm' was deprecated and instead we should use 'celegans'. As usual, information content data was updated. Read More: 2984 Words ... [Read more...]

I've just finished reading Beautiful Data (published by O'Reilly in 2009), a collection of essays edited by Toby Segaran and Jeff Hammerbacher. The 20 essays from 39 contributors address a diverse array of topics relating to data and how it's collected, analysed and interpreted. Since this is a collection of essays, the writing ... [Read more...]

by Joseph Rickert In his new book, The Master Algorithm, Pedro Domingos takes on the heroic task of explaining machine learning to a wide audience and classifies machine learning practitioners into 5 tribes*, each with its own fundamental approach to learning problems. To the 5th tribe, the analogizers, Pedro ascribes the ... [Read more...]

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Is it time to spin up a new instance of Shiny Server? This tutorial is baseed on a fresh install of Ubuntu Server 14.04, but I’m sure it could be tweaked to work on RHEL or CentOS as well. There’s no real secret sauce to the install but there ... [Read more...]

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By Steph Locke We polled our consultants for their tips on how to be more effective at writing R code; and here are the top 10! 10. Don’t pre-emptively tidy Spending time on formatting as you go along gives you … Continue reading → [Read more...]

When modeling the frequency measure in the operational risk with regressions, most modelers often prefer Poisson or Negative Binomial regressions as best practices in the industry. However, as an alternative approach, Quasi-Poisson regression provides a more flexible model estimation routine with at least two benefits. First of all, Quasi-Poisson regression ... [Read more...]

In the mathematical statistics course today, we started talking about tests, and decision rules. To illustrate all the concepts introduced today, we considered the case where we have a sample  with . And we want to test   against  In the course, we’ve seen that we could use a test based ... [Read more...]

An easy way to run R code in parallel on a multicore system is with the mclapply() function. Unfortunately, mclapply() does not work on Windows machines because the mclapply() implementation relies on forking and Windows does not support forking. Previously, I published a hackish solution that implemented a fake mclapply() ... [Read more...]

by Andrie de Vries The second week of SQLRelay (#SQLRelay) kicked off in London earlier this week. SQLRelay is a series of conferences, spanning 10 cities in the United Kingdom over two weeks. The London agenda included 4 different streams, with tracks for the DBA, BI and Analytics users, as well as ... [Read more...]

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I’ll keep this post short and sweet. Here’s some code to get a really nice looking plot in R. It has a high pixel count to produce a high resolution output that can be used in a word document. Because of this, the size of everything in the ... [Read more...]

In this post we will introduce the Fourier basis functions in the context of Functional Data Analysis. The Fourier basis function is method to smooth out data varying over a continuum and exhibiting a cyclical trend. Smoothing techniques play an important role in Functional Data Analysis (FDA) as they provide ... [Read more...]

I was delighted by yesterday's announcement that Angus Deaton has been awarded the Nobel Prize in Economic Science this year. His contributions have have been many, fundamental, and varied, and I certainly won't attempt to summarize them here. Suffice to say that the official citation says that the award is "... [Read more...]

I was delighted by yesterday's announcement that Angus Deaton has been awarded the Nobel Prize in Economic Science this year. His contributions have have been many, fundamental, and varied, and I certainly won't attempt to summarize them here. Suffice to say that the official citation says that the award is "... [Read more...]

The nodes have been assigned a color by the author so that the underlying distinctions are more pronounced. Cars that are perceived as Economical (in aquamarine) are not seen as Sporty or Powerful (in cyan). The red edges connecting these attributes indicate negative relationships. Similarly, a Practical car (in light ... [Read more...]

The nodes have been assigned a color by the author so that the underlying distinctions are more pronounced. Cars that are perceived as Economical (in aquamarine) are not seen as Sporty or Powerful (in cyan). The red edges connecting these attributes in... [Read more...]