https://github.com/audy/richardson-2014

Analysis code for the DIPP microbiome study
https://github.com/audy/richardson-2014

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Analysis code for the DIPP microbiome study

• Host: GitHub
• URL: https://github.com/audy/richardson-2014
• Owner: audy
• Created: 2014-03-03T16:53:40.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2018-03-22T14:01:59.000Z (over 6 years ago)
• Last Synced: 2023-03-11T01:22:20.241Z (over 1 year ago)
• Language: R
• Homepage: http://dipp.utu.fi
• Size: 259 KB
• Stars: 0
• Watchers: 3
• Forks: 2
• Open Issues: 6
• Metadata Files:
  • Readme: readme.md

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README

        
# DIPP Turku Analysis

After cloning this repo, download the data:

`git submodule update --init --recursive`

# Installation

R v3.1.1 with dependencies:

- Phyloseq 

```R

source("http://bioconductor.org/biocLite.R")

biocLite("phyloseq") # grab some tea

```

- dplyr, plyr, ggplot2, reshape2, magrittr

```R

install.packages(c('dplyr', 'plyr', 'ggplot2', 'reshape2', 'magrittr'))

```

## Instructions for generating figures

All figures require an RData file which contains the OTU abundance data as well

as sample metadata. This file is created using the script `bin/write-rdata`. To

generate the RData used in this work, run the command `make dipp-rf-uniq.RData`

from the `R/` directory.

### Figure 1 - Time Series Analysis (GLM)

`make glms`

### Figure 2 - Time Series Analysis (sliding window)

`make sliding_window`

### Figure 3 - 16S, 23S rRNA Phylogenetic tree

I didn't automate this step. Sorry.

### Figure 4 - Timing of Autoimmunity

`make autoimmunity-timing.pdf`

## License

The MIT License (MIT)

Copyright (c) 2014 Austin G. Davis-Richardson

Permission is hereby granted, free of charge, to any person obtaining a

copy of this software and associated documentation files (the

"Software"), to deal in the Software without restriction, including

without limitation the rights to use, copy, modify, merge, publish,

distribute, sublicense, and/or sell copies of the Software, and to

permit persons to whom the Software is furnished to do so, subject to

the following conditions:

The above copyright notice and this permission notice shall be included

in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS

OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF

MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.

IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY

CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,

TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE

SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.