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The latest Sister Claire live-write started 19 hours ago at Fri, 27 Mar 2015 17:41. The URL is:
https://docs.google.com/document/d/1qpj_QxQSRWMbd_S1PVHAM4aBpb-RrskMIqcMHS4i0F0/edit

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## The following two functions allow the use to edgeR's infrastructure
## to execute the DESeq method. Instead of glmFit(dge, design), use
## glmFit.CountDataSet(cds, design), then continue as with a normal
## edgeR analysis.
getOffset.CountDataSet <- function(y) {
  if (any(is.na(sizeFactors(y))))
    stop("Call estimateSizeFactors first")
  log(sizeFactors(y)) - mean(log(sizeFactors(y))) + mean(log(colSums(counts(y))))
}

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#!/bin/bash
# -*- mode:python -*-
#PBS -l nodes=1:ppn=8,mem=30gb
''''/bin/true
# This is bash code to set up the environment
echo "Hello from bash!"
echo "Args are: $@"
# Bash setup code ends here
python - "$@" <<EOF
''' # Python starts here '''

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#!/bin/sh
# -*- mode:R -*-
#PBS -l nodes=1:ppn=8,mem=30gb

'\' >/dev/null 2>&1 || true
# This is bash code to set up the environment

echo "Hello from bash!"
echo "Args are: $@"

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## This will allow you to use dplyr functions with Bioconductor's
## S4Vectors::DataFrame class. They simply call "as.data.frame" on
## DataFrame objects and then pass them to the methods for
## "data.frame". Note that this entails conversion of S4 vector
## columns to primitive vectors. No attempt is made to convert the
## results back to DataFrame, since such a conversion would not
## restore S4 vector columns that were converted to primitive vectors.

library(S4Vectors)
library(dplyr)

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subsetListOfArrays <- function (object, i, j, IJ, IX, I, JX, J) {
    len <- vapply(object, length, 0)
    I <- intersect(I, names(len)[len > 1L])
    J <- intersect(J, names(len)[len > 1L])
    if (missing(i)) {
        IX <- I <- character(0)
        if (missing(j)) 
            IJ <- character(0)
    }
    else {

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#!/usr/bin/env Rscript

library(matrixStats)
library(plyr)
library(lubridate)
library(reshape2)
library(minfi)
library(limma)
library(sva)
library(celltypes450)

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Homebrew build logs for pcre2 on "CentOS release 6.7 (Final)"
Build date: 2016-06-14 13:49:25

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---
title: "Random Plot Order Test"
author: "Ryan C. Thompson"
date: "February 1, 2017"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

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Keybase proof

I hereby claim:

• I am darwinawardwinner on github.
• I am rcthompson (https://keybase.io/rcthompson) on keybase.
• I have a public key ASBVf3s3y1AIHHATFqG8c6WHdw8t4PpcbMIsc2slD2-XBwo

To claim this, I am signing this object: