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Added support for MethylationEPIC assays
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jenzopr committed Feb 23, 2018
1 parent 756bb47 commit cb00e1ed3e9695ee6e4fe8bca4038e79e700661a
Showing with 1,733,807 additions and 94 deletions.
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  3. +866,837 −0 data/ilmn10b2.hg19.sorted.igv.bed
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  5. +16 −9 docs/install.md
  6. +24 −0 environment.yaml
  7. +19 −19 src/admire
  8. +8 −9 src/assembleMvalues.R
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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.
ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K and Infinium MethylationEpic assays.

Use ADMIRE online: https://bioinformatics.mpi-bn.mpg.de

@@ -24,20 +24,27 @@ We have a extensive documentation with a use case available [here](http://admire
Installation and Command-line usage
-----------------------------------

Make sure all prerequisites are met:
We recommend to install prerequisites using the conda package manager. Make sure to have `conda` installed, e.g. via

* [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)
- [Miniconda](https://conda.io/miniconda.html)
- download the Miniconda installer for **Python 3**
- run ```bash Miniconda3-latest-Linux-x86_64.sh``` to install Miniconda
- Answer the question "Do you wish the installer to prepend the Miniconda install location to PATH in your /home/.../.bashrc ?" with yes
OR do ```PATH=dir/to/miniconda3:$PATH``` after installation process

Install admire locally by running:
Clone the ADMIRE repository and populate an environment with all prerequisites:

git clone https://github.molgen.mpg.de/loosolab/admire
export PATH=$PATH:dir/to/admire/src
```bash
$ git clone https://github.molgen.mpg.de/loosolab/admire
$ conda env create -f admire/environment.yaml
$ export PATH=$PATH:dir/to/admire/src
```

Every time you intent to use ADMIRE, make sure the environment is activated:

```bash
$ source activate admire
$ admire -h
Usage: admire [options]
Available options:

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