|ODIN-0.4.1||GPL v3 licence, bigfixes|
|ODIN-0.4||improvement of read extension size estimation|
|ODIN-0.3.2||support of Mac OS, small bugfix, when input-DNA does not overlap with IP-DNA|
|ODIN-0.3.1||use HMM of package hmmlearn instead of sklearn|
|ODIN-0.3||p-value correction, bugfixes, output directory|
|ODIN-0.2||bugfixes, additional narrowPeak output|
|fix chrom size bug, BigWig construction. Since peaks are not merged, please do not use this version!
Feel free to post your question in our googleGroup or write an e-mail: email@example.com
ODIN’s installation setup will automatically install all python package requirements. However, we highly recommend that you pre-install scipy and numpy. The python package requirements are:
- Python >= 2.7
- Numpy >= 1.4.0
- Scipy >= 0.7.0
- Scikit-learn >= 0.14
- Pysam >= 0.7.5
- HTSeq >= 0.6.1
- hmmlearn >= 0.0.1
Important: ODIN uses wigToBigWig from the UCSC utilities website to handle BigWig files. ODIN therefore automatically copies this tool in your bin directory. The wigToBigWig version ODIN copies is for a 64bit linux system. If you have another system (32bit, macsOS), please copy the appropriate binaries by yourself and make sure that they are contained in your $PATH variable. You can load the BigWig files in IGV to visualize the experiment.
ODIN is tested with Python 2.7.6, Numpy 1.8.1, Scipy 0.13.3, Scikit-lean 0.15.2, Pysam 0.7.5, mpmath 0.18 and hmmlearn 0.1.1 on a 64bit Linux (Ubuntu) machine.
If you do not have superuser rights on your system, you can install ODIN by:
python setup.py install --prefix=<INSTALLATION-FOLDER> --rgt-tool=ODIN
Make sure that your PATH variable contains <INSTALLATION-FOLDER>.
A folder rgtdata, containing annotation files such as chromosome sizes, will be created in your homefolder. You can change the path with
Please see here for more information about the rgtdata folder.