Major update of the scripts in this repository #10
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jzthree
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Oct 10, 2022
README.md
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| Sequence class scores can be obtained from Sei chromatin profile predictions. There are 2 types of scores that can be computed: | ||
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| The two `*.tsv` files are the final formatted outputs, while the `chromatin-profiles-hdf5` directory contains the intermediate HDF5 and row label files outputted from Selene from running the Sei deep learning model. | ||
| - Raw sequence class scores: For sequences only. **Note** our manuscript uses the Louvain community clustering, whole-genome sequence class annotation of the human genome whenever we apply sequence classes to reference genome sequences, and we encourage the use of these annotations over the raw sequence class scores when possible. Sequence class annotations for hg38 and hg19 (lifted over from hg38) are available for download from [this Zenodo record](10.5281/zenodo.7113989). |
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maybe add more explanation to the score? I write an example here "Raw sequence class scores are projection scores of chromatin profile predictions projected on the unit-length vectors representing each sequence class. This is an intermediate score originally developed for variant score prediction and is made available for use for developing downstream analysis or applications such as using them as a sequence representation. "
jzthree
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Looks good to me! Thanks for implementing the changes!
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Added support for sequence predictions to both chromatin profile prediction and sequence class score prediction. Changed the usage from the previous version of the repository significantly.