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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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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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# featureCounts on exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene")

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 1.16.1

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# -*- mode:debian-control -*-
Package: BSgenome.Mfascicularis.NCBI.Macaca_fascicularis_5.0
Title: Full genome sequences for Macaca fascicularis (Macaca_fascicularis_5.0)
Description: Full genome sequences for Macaca fascicularis (Crab-eating Macaque aka Cynomolgus Monkey) as provided by NCBI (Macaca_fascicularis_5.0, 2013-06-12) and stored in Biostrings objects.
Version: 0.1
organism: Macaca fascicularis
species: Crab-eating macaque
provider: NCBI
provider_version: Macaca_fascicularis_5.0
release_date: 2013-06-12

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Sorcerer we have ever known. As it is evident that my people have
advised me wrongly, I will not cast you three people into the dreadful
Garden of the Clinging Vines; but your animals must be driven into the
--
touched they crushed, and our adventurers were indeed thankful to have
escaped being cast among them.

--
"Why, they are driving us toward the Black Pit, into which they
threatened to cast us," replied the kitten. "If I were as big as you

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--
-- Toggle Airport Power Off and On again
--
if (offset of "On" in (do shell script "networksetup -getairportpower en0")) > 0 then
	do shell script "networksetup -setairportpower en0 off"
	do shell script "networksetup -setairportpower en0 on"
end if

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setGeneric("f1", signature=c("a"),
           function(..., a) standardGeneric("f1"))
setMethod("f1", c(a="ANY"), function(..., a) list(a=a, ...))
setMethod("f1", c(a="missing"), function(..., a) callGeneric(a=1, ...))
f2 <- function(b,c,d, a) {
    if (missing(a))
        f1(b=b, c=c, d=d)
    else
        f1(a=a, b=b, c=c, d=d)
}

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(defun my-crm-custom (prompt table &optional predicate require-match initial-input hist def inherit-input-method)
  (loop with return-list = nil
        with next-value = nil
        with def-list = (s-split crm-separator (or def ""))
        with def-list-no-empty-string = (remove "" def-list)
        with def-text = (when def-list-no-empty-string
                          (concat "(" (s-join crm-separator def-list) ")"))
        ;; Need to clear this
        with def = nil
        ;; Save original prompt and construct prompt with defaults

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library(ShortRead)
library(parallel)

tsmsg <- function(...) message(format(Sys.time(), "%Y-%m-%d %H:%M:%OS6"), ": ", ...)

## Like readChild but returns NULL when child is finished, and
## automatically unserializes results.
readChildSafe <- function(child) {
    res <- parallel:::readChild(child)
    if (is.integer(res) || is.null(res)) {

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Process:         trash [55738]
Path:            /usr/local/bin/trash
Identifier:      trash
Version:         ???
Code Type:       X86-64 (Native)
Parent Process:  bash [46897]
Responsible:     iTerm [32951]
User ID:         501

Date/Time:       2014-07-17 15:26:41.087 -0700