DeepTCR
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sidhomj
Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
Bumps [numpy](https://github.com/numpy/numpy) from 1.18.0 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...
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Hi, This package has been usefully but I had a suggestion for the UMAP_Plot(). When showing the legend for the UMAP plot it would be nice to be able to...
Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.7.0 to 2.7.2. Release notes Sourced from tensorflow's releases. TensorFlow 2.7.2 Release 2.7.2 This releases introduces several vulnerability fixes: Fixes a code injection in saved_model_cli (CVE-2022-29216) Fixes...
Hello Mr. Sidhom, thank you for creating DeepTCR! I am using the supervised Sequence Classifier, including HLA Supertypes for Samples from different Patients and Treatments. My Question now is: Is...
Hello, I would like to train a supervised model with known antigen specificity, then use that model to classify new TCR sequences as potentially targeting certain antigens. I have followed...
Thanks for writing this package. This package is very useful. To check if I wrote the test code correctly, I used the training set as an independent test set for...
Hello, We are interested in running this tool on our TCR seq data. We have multiple cohorts of cancer patients, responders and non-responders plus a big cohort of COVID patients,...
Hi, thank you for creating this great tool! I was wondering if you could offer some guidance on handling large datasets in the unsupervised workflow? In particular this seems to...
Hi. Is the dropout probability in Convolutional_Features() 0.0 when training the unsupervised model? If not, where is this probability defined? And did I understand correctly that there is no pooling...
Hello @sidhomj, I used the unsupervised partof DeepTCR to cluster TCR sequences, but when I allowed the method to determine the optimal threshold parameter with the following command line, I...
