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jenzopr committed Oct 20, 2015
1 parent 26a744d commit cf86ccbd390f4d9fb175a8e136c9c09e95ee5cf4
Showing with 97 additions and 5 deletions.
  1. +11 −1 docs/custom.md
  2. +1 −1 docs/genesets.md
  3. +1 −1 docs/hiscan.md
  4. +3 −1 docs/index.md
  5. +28 −0 docs/parameters.md
  6. +12 −1 docs/regions.md
  7. +38 −0 docs/test.html
  8. +3 −0 mkdocs.yml
@@ -1,4 +1,14 @@
ADMIRE is also able to process a tab-separated sample definition file, with the following columns:

column | explanation
-------|------------
sample_id | an arbitrary sample identifier. Note that corresponding green and red channel files need the same identifier.
file | relative or absolute path of a red or green channel idat file.
channel | indicates whether the file is from the red or green channel (can be *Red* or *Grn*).
sample_group | an arbitrary string identifying the sample group of the sample.

For example, the sample definition file could look like:

```
sample_id file channel sample_group
1 8769527070/8769527070_R01C01_Grn.idat Grn control
@@ -7,5 +17,5 @@ sample_id file channel sample_group
3 8769527070/8769527070_R02C01_Red.idat Red treatment
```

ADMIRE can then be called with `admire -s sample_definition.txt` and will look the *.idat files specified in the sample definition file.
ADMIRE can then be called with `admire -s sample_definition.txt` and will look for the \*.idat files specified in the sample definition file.

@@ -1 +1 @@
Gene sets can be given with admire -g geneset1 -g geneset2 .... Gene set files should be in *.gmt format, as provided by MSigDB [4].
Gene sets can be given with `admire -g geneset1 -g geneset2 ...`. Gene set files should be in *.gmt format, as provided by (MSigDB)[http://www.broadinstitute.org/gsea/msigdb/index.jsp].
@@ -7,4 +7,4 @@ To use the files generated by the scanner system with ADMIRE, all file directori

ADMIRE can then be called with `admire -c SampleSheet.csv -z compressFileName.tar.gz`

*Hint*: ADMIRE can also read files ending on *.zip or *.tbz2.
*Hint*: ADMIRE can also read files ending on \*.tar.gz, \*.tgz or \*.tbz2.
@@ -26,7 +26,9 @@ Features
How to cite?
------------

Please cite Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. *???* (**2015**) when using admire in your work.
Please cite the paper describing ADMIRE when using the web service or command line version in your research:

Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay. *???* (**2015**) when using admire in your work.

Contribute
----------
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Here we list all current parameters for command-line usage and their explanation:

```
Usage: admire [options]
Available options:
-c | Comma separated sample definition file (SampleSheet.csv)
-s | Tab separated sample definition file (design.txt)
-z | Compressed input of idat files (requires -c).
-e | Create quality control report in PDF
-r | Region file in bed format (regions.bed), use multiple -r parameters to calculate for multiple region files
-p | Detection p-value to exclude probes prior to analysis (0.01)
-t | Exclude probes where more than t% samples failed according to the detection p-value. (0.4)
-n | Normalization method (fn,swan,noob,illumina,raw,quantile)
-b | In case of functional normalization, skip noob background correction step
-d | In case of noob or functional normalization, skip dye correction step
-f | In case of quantile normalization, skip fixing outliers prior to analysis
-l | In case of quantile normalization, label samples as bad if their median signals are below a given value (10.5)
-m | In case of quantile normalization, remove bad samples
-q | Q-value cutoff for multiple testing correction (0.05)
-i | Render advanced plots for the best i regions (20)
-g | Gene set file for enrichment analysis, use multiple -g parameters to calculate enrichment over many gene sets
-o | tar-gz compress output into file given
-h | shows this help message
-v | shows version information
Options -c and -s are mutually exclusive.
```
@@ -1 +1,12 @@
Custom genomic regions should be provided in BED format and can be given by admire -r regions1.bed -r regions2.bed ...
Custom genomic regions should be provided in BED format and can be given by `admire -r regions1.bed -r regions2.bed ...`.

*Hint*: Use multiple `-r` parameters to analyse more than one region at a time.
*Hint*: The BED format is described [here](http://www.ensembl.org/info/website/upload/bed.html)

To enable the Gene Set Enrichment Analysis for a certain bed file, include a *gene_name* property in column 4 of the bed file:

```
chr1 213941196 213942363 gene_name=gene1
chr1 213942363 213943530 gene_name=gene2
chr1 213943530 213944697 gene_name=gene3
```
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta http-equiv="Content-Style-Type" content="text/css" />
<meta name="generator" content="pandoc" />
<title></title>
<style type="text/css">code{white-space: pre;}</style>
</head>
<body>
<h1 id="welcome-to-the-admire-documentation">Welcome to the ADMIRE documentation</h1>
<p>ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.</p>
<p>Use ADMIRE online: <a href="https://bioinformatics.mpi-bn.mpg.de">bioinformatics.mpi-bn.mpg.de</a></p>
<h2 id="overview-and-objective">Overview and Objective</h2>
<p>DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and the stage of a disease. Besides whole genome bisulfit sequencing, Illumina HumanMethylation450K Assays represent a versatile and cost-effective tool to investigate changes of methylation patterns at CpG sites. ADMIRE was developed as an open source, semi-automatic analysis pipeline and visualization tool for Illumina HumanMethylation450K Assays.</p>
<h2 id="features">Features</h2>
<ul>
<li>Automatic filtering and normalization</li>
<li>Statistical testing and multiple testing correction</li>
<li>Supports arbitrary number of samples and sample groups</li>
<li>Differential methylation analysis on pre-calculated and individual genomic regions</li>
<li>Provides ready-to-plug-in files for genome browsers (like IGV)</li>
<li>Provides publication-ready figures for the most differentially methylated regions</li>
<li>Performs gene set enrichment analysis on predefined and individual gene sets</li>
</ul>
<h2 id="how-to-cite">How to cite?</h2>
<p>Please cite Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. <em>???</em> (<strong>2015</strong>) when using admire in your work.</p>
<h2 id="contribute">Contribute</h2>
<ul>
<li>Issue Tracker: https://github.molgen.mpg.de/loosolab/admire/issues</li>
<li>Source Code: https://github.molgen.mpg.de/loosolab/admire</li>
</ul>
<h2 id="support">Support</h2>
<p>If you are having issues, please feel free to send an e-mail to Jens Preußner (jens.preussner@mpi-bn.mpg.de).</p>
<h2 id="license">License</h2>
<p>The project is licensed under the MIT license.</p>
</body>
</html>
@@ -1,4 +1,6 @@
site_name: ADMIRE
site_description: 'Analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay.'
site_author: 'Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso'
repo_url: https://github.molgen.mpg.de/loosolab/admire
repo_name: 'GitHub'
pages:
@@ -13,5 +15,6 @@ pages:
- 'Custom input': 'custom.md'
- 'Genomic regions' : 'regions.md'
- 'Gene sets' : 'genesets.md'
- 'Available parameters' : 'parameters.md'
- Output: 'output.md'
- 'MIT License': 'license.md'

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