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| ADMIRE - Analysis of DNA methylation in genomic regions | |
| ======================================================= | |
| ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips. | |
| 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 methylation analysis on pre-calculated and individual genomic regions | |
| - Provides ready-to-plug-in files for genome browsers (like IGV) | |
| - Provides publication-ready figures for the most differentially methylated regions | |
| - Performs gene set enrichment analysis on predefined and individual gene sets | |
| Documentation | |
| ------------- | |
| We have a extensive documentation with a use case available [here](http://admire.readthedocs.org). | |
| Installation and Command-line usage | |
| ----------------------------------- | |
| Make sure all prerequisites are met: | |
| * [comb-p](https://github.com/brentp/combined-pvalues) | |
| * [bedtools](https://github.com/arq5x/bedtools2) | |
| * [R/Rscript](http://www.r-project.org/) | |
| * [python - numpy](http://continuum.io/downloads) | |
| * [python - matplotlib](http://continuum.io/downloads) | |
| Install admire locally by running: | |
| git clone https://github.molgen.mpg.de/loosolab/admire | |
| export PATH=$PATH:dir/to/admire/src | |
| ```bash | |
| 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. | |
| ``` | |
| How to cite? | |
| ------------ | |
| Please cite Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay. *Epigenetics & Chromatin* (**2015**), doi:10.1186/s13072-015-0045-1, when using admire in your work. | |
| Contribute | |
| ---------- | |
| - Issue Tracker: github.molgen.mpg.de.com/loosolab/admire/issues | |
| - Source Code: github.molgen.mpg.de.com/loosolab/admire | |
| Support | |
| ------- | |
| 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. |