Robert M Flight rmflight

Notes:

I've tried to break up in to separate pieces, but it's not always possible: e.g. knowledge of data structures and subsetting are tidy intertwined.
Level of Bloom's taxonomy listed in square brackets, e.g. http://bit.ly/15gqPEx. Few categories currently assess components higher in the taxonomy.

Programming R curriculum

Ensemble Inference and Inferability of Gene Regulatory Networks|http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0103812 Genomic responses in mouse models greatly mimic human inflammatory diseases|http://www.pnas.org/content/early/2014/07/31/1401965111.full.pdf IVT-seq reveals extreme bias in RNA sequencing|http://genomebiology.com/2014/15/6/R86 DiffSplice: the genome-wide detection of differential splicing events with RNA-seq|http://nar.oxfordjournals.org/content/41/2/e39.full FDM: a graph-based statistical method to detect differential transcription using RNA-seq data|http://bioinformatics.oxfordjournals.org/content/27/19/2633.full MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery|http://nar.oxfordjournals.org/content/38/18/e178.full A probabilistic framework for aligning paired-end RNA-seq data|http://bioinformatics.oxfordjournals.org/content/26/16/1950.full

test1

	```{r defineFunct}

	insertStoreText <- function(inObj, inText){
	cat(inText)
	inObj <- c(inObj, inText)
	return(inObj)
	}

	inObj <- character(0)
	```

	<!DOCTYPE html>
	<html>
	<head>
	<!--begin.rcode setTitle, echo=F
	title <- "test me"
	end.rcode-->
	<title>
	<!--begin.rcode genTitle, results='asis', echo=F
	cat(title)
	end.rcode-->

	This is a test file that I'm working
	with to see if I can modify it
	after getting a personal OAuth token
	todays date is:Fri Jun 14 2013 14:59:30 GMT-0400 (Eastern Daylight Time)count: 1; date: Fri Jun 14 2013 20:42:59 GMT-0400 (Eastern Daylight Time)
	Sat Jun 15 2013 17:02:50 GMT-0400 (Eastern Daylight Time)
	Sat Jun 15 2013 17:02:51 GMT-0400 (Eastern Daylight Time)
	Sat Jun 15 2013 17:06:30 GMT-0400 (Eastern Daylight Time)
	Mon Jun 17 2013 21:40:18 GMT-0400 (Eastern Daylight Time)
	Mon Jun 17 2013 21:40:52 GMT-0400 (Eastern Daylight Time)
	Fri Oct 04 2013 08:33:59 GMT-0400 (EDT)

	```{r t1}
	crud <- "alksdjflkajsdflkajsdf"
	```

	Here is some text for context

	```{r t2, echo=FALSE, results='asis'}
	cat(paste("```",crud,"```", sep="\n"))
	```

	# assumes that a ccCompareResult object has been generated from a ccEnrichResult, eg ccResults from the vignette
	# note that the $BP is to access a single ccCompareResult from a collection, these are generally BP, MF, CC, KEGG, etc

	library(graph)
	tmpGraph <- mainGraph(ccResults$BP)
	tmpData <- nodeData(tmpGraph, , "listMembership")

	go2list <- data.frame(goid = names(tmpData), listMembership = unlist(tmpData), stringsAsFactors=FALSE)

	#!/path/2/Rscript

	# License: CC0 (just be nice and point others to where you got this)
	# Author: Robert M Flight <[email protected]>, github.com/rmflight
	#
	# This is a post-commit hook that after a successful commit subsequently increments the package version in DESCRIPTION
	# and commits that. Analogous to the pre-commit at https://gist.github.com/rmflight/8863882, but useful if you only have
	# good reasons for not doing it on the pre-commit.
	#
	# To install it, simply copy this into the ".git/hooks/post-commit" file of your git repo, change /path/2/Rscript, and make