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Added Google Colab link to README.md
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README.md

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@@ -27,29 +27,31 @@ For sequences longer than 40 amino acids, TADA_T2 uses a 'sliding window' approa
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For sequences shorter than 40 amino acids, TADA_T2 will pad the sequence with 'X' amino acids to make the sequence 40 amino acids long. You can choose to pad the sequence evenly or on the N- or C-terminus. Further, you can pad the sequence with just G and S or a random selection of amino acids. **This is NOT ideal** and we recommend that you do not use TADA_T2 to predict TAD scores for sequences shorter than 40 amino acids. However, this functionality is available for users if you set ``safe_mode=False``. Because the predictor was not made for this, the predictions may not be accurate. Thus, by default we restrict the availablity of this feature.
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## How can I cite TADA or TADA_T2?
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Please cite the original publication at https://www.nature.com/articles/s41586-024-07707-3. If you use TADA_T2, please mention in your methods that you used TADA_T2 to generate your predictions and link to this repository so your readers know exactly how you got your results and so that they can use TADA_T2 if they would like to.
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Please cite the [original publication](https://www.nature.com/articles/s41586-024-07707-3). If you use TADA_T2, please mention in your methods that you used TADA_T2 to generate your predictions and link to this repository so your readers know exactly how you got your results and so that they can use TADA_T2 if they would like to.
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### Citation:
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Morffy, N., Van den Broeck, L., Miller, C. et al. Identification of plant transcriptional activation domains. Nature 632, 166–173 (2024). https://doi.org/10.1038/s41586-024-07707-3
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[Morffy, N., Van den Broeck, L., Miller, C. et al. Identification of plant transcriptional activation domains. Nature 632, 166–173 (2024)](https://doi.org/10.1038/s41586-024-07707-3)
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## Using TADA in Google Colab
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Basic functionality of TADA_T2 is also available in [Google Colab](https://colab.research.google.com/drive/1g4tkklihI-dIZV5BEHpPgpqtvofw1BFV?usp=sharing). This let's you generate TADA scores from sequences or from .fasta files without having to locally intall TADA_T2!
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# Installation
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To install from PyPI, run:
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```bash
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pip install TADA-T2
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pip install TADA-T2
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```
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You can also install the current development version from
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```bash
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pip install git+https://git@github.com/ryanemenecker/TADA_T2
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pip install git+https://git@github.com/ryanemenecker/TADA_T2
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```
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To clone the GitHub repository and gain the ability to modify a local copy of the code, run
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```bash
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git clone https://github.com/ryanemenecker/TADA_T2.git
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cd TADA_T2
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pip install -e .
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git clone https://github.com/ryanemenecker/TADA_T2.git
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cd TADA_T2
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pip install -e .
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```
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# Usage

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