1258 search results for "tutorial"

Quality trimming in R using ShortRead and Biostrings

March 3, 2010
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I wrote an R function to do soft-trimming, right clipping FastQ reads based on quality.This function has the option of leaving out sequences trimmed to extinction and will do left-side fixed trimming as well.#softTrim#trim first position lower than minQuality and all subsequent positions#omit sequences that after trimming are shorter than minLength#left trim to firstBase, (1 implies no left trim)#input:...

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Arrange multiple ggplot2 plots in the same image window

March 3, 2010
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In a previous tutorial I showed you how to create plots faceted by the level of a third variable using ggplot2. A commenter asked about using faceted plots and viewports and reminded me of this function I found in the ggplot2 Google group. The arrange function below is similar to using par(mfrow=c(r,c)) in base graphics to put more than...

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Happy Birthday GGD! The 10 Most Popular Posts Since GGD’s Launch

February 23, 2010
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The first post on Getting Genetics Done was one year ago today. To celebrate, here are the top 10 most viewed posts since GGD launched last year. Incidentally, nine of the ten are tutorials on how to do something in R. Thanks to all the readers and all...

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Getting Started with Sweave: R, LaTeX, Eclipse, StatET, & TeXlipse

February 23, 2010
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Getting Started with Sweave: R, LaTeX, Eclipse, StatET, & TeXlipse

Being able to press a single button that runs all your statistical analyses and integrates the output into your final report is a beautiful thing. If you have not already heard, this is what Sweave can do for you. However, getting your computer to run ...

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Getting Started with Sweave: R, LaTeX, Eclipse, StatET, & TeXlipse

February 23, 2010
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Getting Started with Sweave: R, LaTeX, Eclipse, StatET, & TeXlipse

Being able to press a single button that runs all your statistical analyses and integrates the output into your final report is a beautiful thing. If you have not already heard, this is what Sweave can do for you. However, getting your computer to run ...

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The R type system

February 21, 2010
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The R type system

R is a weird beast. Through it's ancestor the S language, it claims a proud heritage reaching back to Bell Labs in the 1970's when S was created as an interactive wrapper around a set of statistical and numerical subroutines. As a programming language,...

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Artificial Immune Systems and Financial Applications?

February 11, 2010
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Artificial Immune Systems and Financial Applications?

One of the buzzwords that seems to be common these days is AIS or Artificial Immune Systems. It is a biologically inspired classification type system that essentially tries to replicate some of our own natural immune system algorithms. Our bodies hav...

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Using J48 Decision Tree Classifier to Dynamically Allocate Next Day Position in Stocks or Bonds

February 11, 2010
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Using J48 Decision Tree Classifier to Dynamically Allocate Next Day Position in Stocks or Bonds

The prior introduction using a simple model to determine next weeks change based on the S&P 500 index and VIX did not look very promising, although hopefully it served to familiarize yourself with how classification is used in augmenting trading decisi...

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Video: What is R?

February 10, 2010
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By popular demand, we've made the video of our 30-minute webcast "The R Project" available on YouTube so that everyone can easily watch it. If you (or a friend!) have ever wondered what this R thing is all about, this is the video for you. Here's the first part: Because of YouTube restrictions it's split up into four parts,...

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Linux Server Profiling: Using Open Source Tools For Bottleneck Analysis

February 9, 2010
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This tutorial covers profiling of Linux servers using open-source tools such as "iostat", "oprofile" and "blktrace". Both processor-bound and I/O-bound cases are covered, and the emphasis is on tools that provide visual displays of relevant metrics. Li...

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