Initial upload

.gitignore

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+proteinGroups.txt
+*.fastq
+*.gz

R/README.md

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+# R Code
+
+Use this directory to place R scripts with R code that is specific to the project.  General re-usable R code should probably be put into an R package but one-off functions can be placed here. 
+

R/helper_functions.R

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+factor_colours <- function(values){
+  f=factor(values)
+  rainbow(length(levels(f)))[as.integer(f)]
+}

README.md

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-# project-template
-Template for Data Analysis Projects
+#Data Analysis Project Template
+
+This is your project readme file.  You can have other readme files but this one will be displayed at the root of your github repository.  This file serves as the entry point for people who want to check out your repository.  They should be able to read this an rerun your analyses.
+
+
+

bin/README.md

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+# Scripts and other programs
+
+If you write non-trivial scripts to perform your analysis include those scripts here.

example.Rmd

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+---
+title: "Example Analysis"
+output: html_document
+---
+
+```{r global_options, include=FALSE}
+knitr::opts_chunk$set(fig.width=12, fig.height=8,
+                      echo=FALSE, warning=FALSE, message=FALSE)
+knitr::opts_chunk$set(cache=FALSE)
+options(width = 60)
+library(ggplot2)
+library(stringr)
+library(dplyr)
+library(tidyr)
+```
+
+Example analysis
+
+```{r read_data}
+	table <- read.table("raw_data/counts.txt")
+```
+
+```{r make_figure}
+
+```

figures/README.md

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+# Figures
+
+Often the result of an R script is a figure to be included in a paper or presentation.  Send your figure outputs to this directory

hpc/README.md

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+# HPC Processing
+
+Many project require extensive processing of very large data files before an R based data analysis can begin.  Those steps should be captured in this directory.  Typically this would include
+
+- Instructions on obtaining the raw data
+- Shell scripts or pipeline code used to process the raw data
+- README files documenting how to run the pipeline steps (perhaps showing the order of steps) and documenting any other commands that need to be run
+

raw_data/README.md

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+# Raw Data
+
+This directory is for analysis ready files that we treat as raw data for the purpose of R analysis.  For example RNA-seq counts files or `proteinGroups.txt` files fall in this category.  They should not be checked in to git but this readme should provide details of how to get them.  For example, in a code block like this;
+
+`proteinGroups.txt` can be obtained as follows;
+
+```bash
+	wget https://www.dropbox.com/s/dsnp6cmn/proteinGroups.txt?dl=0 -O proteinGroups.txt
+```
+
+Or if the data is private or requires authentication provide a link to the website where the user can interactively download the file.
+

results/README.md

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+# Intermediate Results
+
+This directory contains intermediate files that are produced as part of an analysis.  These intermediate files should not be checked in to git but you may also place shell scripts or other code for intermediate file processing here.  Those shell scripts should be checked in.
+