MLL-ENL tutorial workflow¶
You can download the raw dataset along with all the notebooks (approx 43 MB) for this example using following link: Download
Extract the downloaded mll_enl.zip file to any folder. Once extracted, you will find the following directory structure:
. ├── analysis_data ├── notebooks │ ├── 1_preprocessing.ipynb │ ├── 2_mapping.ipynb │ ├── 3_markers.ipynb │ └── 4_control_mappings.ipynb └── raw_data ├── MLL_ENL │ ├── barcodes.tsv │ ├── genes.tsv │ └── matrix.mtx └── WT ├── barcodes.tsv ├── genes.tsv └── matrix.mtx
Files with .ipynb extension are notebook files. If you do not already have a
jupyter notebook server running, then open your terminal and type
notebook. Your browser should open a new window automatically. Navigate to
the notebook location and launch the notebooks. Start with
1_preprocessing.ipynb. That needs to be run first, followed by 2_mapping.
After that, the last two notebooks can be run in any order.
Read static versions of the notebooks here: