Maren CC marencc

Configure Git to use a proxy

In Brief

You may need to configure a proxy server if you're having trouble cloning or fetching from a remote repository or getting an error like unable to access '...' Couldn't resolve host '...'.

Consider something like:

Using Ballgown and Polyester

Ballgown

Reading data

ballgown creates a ballgown object from tablemaker output
ballgownrsem creates a ballgown object from RSEM output. (not yet well-tested).
gffRead and gffReadGR read GTF (annotation) files into R
- gffRead gives you a data frame
gffReadGR gives you a GRanges object

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

Dual axes for ggplot2

Modified from:

https://stackoverflow.com/questions/21026598/ggplot2-adding-secondary-transformed-x-axis-on-top-of-plot

https://rpubs.com/kohske/dual_axis_in_ggplot2

Updated: 2016-07-27

	# modified from http://stackoverflow.com/questions/1401904/painless-way-to-install-a-new-version-of-r-on-windows

	# run on old computer / r version
	setwd("/Users/Florian/Dropbox/temp") # or any other existing temp directory
	packages <- installed.packages()[,"Package"]
	save(packages, file="Rpackages")


	# run on new computer / r version
	setwd("/Users/Florian/Dropbox/temp") # or any other existing temp directory


	# http://www.vincebuffalo.com/blog/2012/03/12/using-bioconductor-to-analyze-your-23andme-data.html

	library(gwascat)
	data(ebicat37)
	library(GenomicRanges)

	data="~/projects/23andme/genome_v4.txt"

	#!/bin/bash

	# check commands: slopBed, bedGraphToBigWig and bedClip

	which bedtools &>/dev/null \|\| { echo "bedtools not found! Download bedTools: <http://code.google.com/p/bedtools/>"; exit 1; }
	which bedGraphToBigWig &>/dev/null \|\| { echo "bedGraphToBigWig not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }
	which bedClip &>/dev/null \|\| { echo "bedClip not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

	# end of checking

	## RNA-seq analysis with DESeq2
	## Stephen Turner, @genetics_blog

	# RNA-seq data from GSE52202
	# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
	# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

	# Import & pre-process ----------------------------------------------------

	# Import data from featureCounts