From 2dd2c2ff18d561d1dd4b899281a0fbc59f5aa8e0 Mon Sep 17 00:00:00 2001 From: jenzopr Date: Tue, 3 Mar 2015 16:27:27 +0100 Subject: [PATCH] Checked for consistency --- DOCUMENTATION.md | 2 +- README.md | 50 ++++++++++++++++++++++++++++++------------------ 2 files changed, 32 insertions(+), 20 deletions(-) diff --git a/DOCUMENTATION.md b/DOCUMENTATION.md index 11f9862..c83670e 100644 --- a/DOCUMENTATION.md +++ b/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) diff --git a/README.md b/README.md index c6d18ab..a83a68e 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ -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 -------- @@ -11,9 +11,14 @@ 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 ----------------------------------- @@ -32,15 +37,23 @@ 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. ``` @@ -48,21 +61,20 @@ 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. \ No newline at end of file +The project is licensed under the MIT license.