Example analyses

Each example analysis is a published study by the Bloom lab. Each analysis is in its own subdirectory in the examples folder on GitHub. Typically there is a Jupyter notebook that performs the analysis.

Here are the analyses:

Doud and Bloom (2016)

Doud et al (2017)

Dingens et al (2017)

Doud et al (2018)

Haddox et al (2018)

Dingens et al (2018)

Lee et al (2018)

Running the examples

Navigate here to access the example analyses and require input data.

To run a Jupyter notebook, you need to install jupyter. Most of the notebooks also have other requirements (such as fastq-dump to download the deep sequencing data from the Sequence Read Archive), and these dependencies are described in the notebooks.

To run a notebook interactively, type:

jupyter notebook analysis_notebook.ipynb

To run a notebook in command-line mode, run:

jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1 analysis_notebook.ipynb

You should not open the notebook while it is being run in command-line mode.

If you are in the Bloom lab and using the Hutch server, you can run a notebook via slurm by creating a file run.sbatch that looks like this:

#PBS -l walltime=24:00:00
jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1 analysis_notebook.ipynb

and then running the file with:

sbatch -p largenode -c 14 --mem=140000 run.sbatch

where the number of CPUs requested with -c should match the number specified for multi-processor operations in the notebook.