Checked for consistency

DOCUMENTATION.md

@@ -179,7 +179,7 @@ ADMIRE -s sample_definition.txt -e quality_report.pdf -r gencode.v19.genes_promo
 
 ### Citation and License
 
-Please cite Preussner J, Kuenne C and Looso, M: Analysis of DNA methylation in genomic regions with ADMIRE. Bioinformatics (2015), doi:tba
+Please cite Preussner J, Kuenne C and Looso, M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. Bioinformatics (2015), doi:tba
 
 #### The MIT License (MIT)
 

README.md

@@ -1,19 +1,24 @@
-admire - Analysis of DNA methylation in genomic regions
+ADMIRE - Analysis of DNA methylation in genomic regions
 =======================================================
 
-admire is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.
+ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.
 
-Use admire online: https://bioinformatics.mpi-bn.mpg.de
+Use ADMIRE online: https://bioinformatics.mpi-bn.mpg.de
 
 Features
 --------
 
 - Automatic filtering and normalization
 - Statistical testing and multiple testing correction
 - Supports arbitrary number of samples and sample groups
-- Differential analysis on pre-calculated and individual genomic regions
+- Differential methylation analysis on pre-calculated and individual genomic regions
 - Provides ready-to-plug-in files for genome browsers (like IGV)
 
+Documentation
+-------------
+
+We have a extensive documentation with a use case available [here](https://github.com/jenzopr/admire/blob/master/DOCUMENTATION.md)
+
 Installation and Command-line usage
 -----------------------------------
 
@@ -32,37 +37,44 @@ Install admire locally by running:
 Usage: admire [options]
 
 Available options:
- -c     comma separated sample definition file (SampleSheet.csv)
- -s     tab separated sample definition file (design.txt)
- -r     region file in bed format (regions.bed)
-        Use multiple -r parameters to calculate for multiple region files
- -n     normalization method (fn)
- -q     q-value cutoff for multiple testing correction (0.05)
- -h     shows this help message.
- -v     shows version information.
- -z     compressed input of idat files (requires -c).
+-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)
+-o | tar-gz compress output into file given
+-h | shows this help message
+-v | shows version information
 
 Options -c and -s are mutually exclusive.
 ```
 
 How to cite?
 ------------
 
-Please cite Preußner J, Kuenne C and Looso M. Title here. *Bioinformatics*, **2015** when using admire in your work.
+Please cite Preussner J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. *Bioinformatics*, **2015** when using admire in your work.
 
 Contribute
 ----------
 
-- Issue Tracker: github.com/$project/$project/issues
-- Source Code: github.com/$project/$project
+- Issue Tracker: github.com/jenzopr/admire/issues
+- Source Code: github.com/jenzopr/admire
 
 Support
 -------
 
-If you are having issues, please let us know.
-We have a mailing list located at: project@google-groups.com
+If you are having issues, please feel free to send an e-mail to Jens Preußner (jens.preussner@mpi-bn.mpg.de).
 
 License
 -------
 
-The project is licensed under the MIT license.
+The project is licensed under the MIT license.