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Fixed URLs for training dataset and tarball to run jupyter notebooks #5

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Fixed URLs for training dataset and tarball to run jupyter notebooks #5

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b01f1d1
Update README.md
ctokheim Jun 3, 2024
1f90581
Update Introduction.ipynb
ctokheim Jun 3, 2024
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4 changes: 2 additions & 2 deletions Introduction.ipynb
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Expand Up @@ -17,7 +17,7 @@
"If you are interested in the mutations CHASMplus used for training, you can download it via wget:\n",
"\n",
"```bash\n",
"$ wget http://karchinlab.org/data/CHASMplus/formatted_training_list.txt.gz\n",
"$ wget https://karchinlab.org/datasets/formatted_training_list.txt.gz\n",
"$ gunzip formatted_training_list.txt.gz\n",
"```\n",
"\n",
Expand All @@ -30,7 +30,7 @@
"Be sure to be in the directory you would like to use for this protocol. The first step is to obtain the example data. You can use the wget command in bash to download the example data. On Mac, you may need to first install the wget command via HomeBrew by brew install wget. In the following command we assume you are in the top-level directory. On windows you will need to download the file from the URL (without wget) and place it in the jupyter notebook directory.\n",
"\n",
"```bash\n",
"$ wget http://karchinlab.org/data/CHASMplus/Tokheim_Cell_Systems_2019.tar.gz\n",
"$ wget https://karchinlab.org/datasets/Tokheim_Cell_Systems_2019.tar.gz\n",
"$ tar xvzf Tokheim_Cell_Systems_2019.tar.gz\n",
"```\n",
"\n",
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -33,10 +33,10 @@ $ jupyter lab

## Data

The notebooks use data and results available [here](http://karchinlab.org/data/CHASMplus/Tokheim_Cell_Systems_2019.tar.gz).
The notebooks use data and results available [here](https://karchinlab.org/datasets/Tokheim_Cell_Systems_2019.tar.gz).
Place the data in the top-level directory of this repository.
The scores for each method in the benchmark are found in the `CHASMplus/data/benchmark` folder. If you are interested
in obtaining the full list of mutations used for training CHASMplus, it is available [here](http://karchinlab.org/data/CHASMplus/formatted_training_list.txt.gz).
in obtaining the full list of mutations used for training CHASMplus, it is available [here](https://karchinlab.org/datasets/formatted_training_list.txt.gz).

## Citation

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