Refined documentation

docs/custom.md

@@ -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.
 

docs/genesets.md

@@ -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].

docs/hiscan.md

@@ -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.

docs/index.md

@@ -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
 ----------

docs/parameters.md

@@ -0,0 +1,28 @@
+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.
+```

docs/regions.md

@@ -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
+```

docs/test.html

@@ -0,0 +1,38 @@
+<!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>

mkdocs.yml

@@ -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'