You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: README.md
+9-7Lines changed: 9 additions & 7 deletions
Original file line number
Diff line number
Diff line change
@@ -27,29 +27,31 @@ For sequences longer than 40 amino acids, TADA_T2 uses a 'sliding window' approa
27
27
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.
28
28
29
29
## How can I cite TADA or TADA_T2?
30
-
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.
30
+
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.
31
31
32
32
### Citation:
33
-
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
33
+
[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)
34
34
35
+
## Using TADA in Google Colab
36
+
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!
35
37
36
38
# Installation
37
39
38
40
To install from PyPI, run:
39
41
```bash
40
-
pip install TADA-T2
42
+
pip install TADA-T2
41
43
```
42
44
43
45
You can also install the current development version from
0 commit comments