Added CRISPR DNA repair outcomes dataset#30
Merged
Conversation
kexinhuang12345
approved these changes
Dec 30, 2020
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Dataset Description: Primary T cells are a promising cell type for therapeutic genome editing, as they can be engineered efficiently ex vivo and transferred to patients. This dataset consists of the DNA repair outcomes of CRISPR-CAS9 knockout experiments on primary CD4+ T cells drawn from 15 donors. For each of the 1,521 unique genomic locations from 553 genes, we provide the 20-nucleotide guide sequence along with the 3-nucletoide PAM sequence.
5 repair outcomes are included for prediction: fraction of indel reads with an insertion, average insertion length, average deletion length, indel diversity, fraction of repair outcomes with a frameshift.
Task Description: Given a DNA sequence, predict the repair outcomes of a CRISPR-CAS9 knockout experiment.
Dataset Statistics: 1,521 DNA sequences (guide+PAM) with 5 repair outcomes for each measured across different donor populations of primary T cells
Dataset Split: Random Split
References: Leenay, Ryan T., et al. "Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells." Nature biotechnology 37.9 (2019): 1034-1037.
License: CC BY 3.0.