Using pip:
download meclass2-0.2.0.tar.gz pip install meclass2-0.2.0.tar.gz
For a user-specific install use --user flag:
pip install --user meclass2-0.2.0.tar.gz
- sklearn >= 0.18
- numpy
- scipy
- seaborn
- matplotlib
- pandas
We recommend installing anaconda or a similar all in one scientific package which will include all of these.
download example_data.tgz tar -xzf example_data.tgz cd example_data
meclass2_interpolation --autosome-only -g refGene_sample.txt -z sample_data_5hmC.bg sample_data_5mC.bg sample_data.expr HRPS_test HRPS
Example run time: ~20-30 minutes
meclass2_classifier --num_trees 1001 -t 5hmC . meclass2_classifier --num_trees 1001 -t 5mC . meclass2_classifier --num_trees 1001 -t 5mC_5hmC .
Example run time: ~3-5 minutes each or faster if using multiple threads (-j option)
meclass2_reporting --plot_results *.pred
Example run time: <1 minute
meclass2_clustering . cluster --tag 5mC_5hmC --numClusters=4 --lowerPredBound=0.75
Example run time: ~1 minute
- There is a warning thrown in the clustering script about a depreciated function (axisbg). This can be safely ignored.