genomekit.yaml

Name: "GenomeKit genomic data"
Description: GenomeKit is Deep Genomics’ Python library for fast and easy access to genomic resources such as sequence, data tracks, and annotations. The goal is to let machine learning researchers build data sets easily, and to be creative about how those data sets are designed. Out of the box, GenomeKit provides access to pre-built optimized genomic data files that are required for its operation.
Documentation: https://deepgenomics.github.io/GenomeKit/data_org.html
Contact: https://github.com/deepgenomics/GenomeKit/issues
ManagedBy: Deep Genomics
UpdateFrequency: Data is updated when popular new genome versions (assemblies or annotations) are released
Tags:
  - genome
  - genomic
  - Homo sapiens
  - Mus musculus
  - non-human primate
  - Rattus norvegicus
  - variant annotation
  - bioinformatics
  - life sciences
  - open source software
License: Apache License Version 2.0 https://www.apache.org/licenses/LICENSE-2.0
Resources:
  - Description: Optimized data files required to query genomic data using GenomeKit (Assemblies, annotations, etc)
    ARN: arn:aws:s3:::genomekit-public-dg
    Region: us-east-1
    Type: S3 Bucket
DataAtWork:
  Tutorials:
  - Title: Quickstart
    URL: https://deepgenomics.github.io/GenomeKit/quickstart.html
    AuthorName: Deep Genomics
  Tools & Applications:
  - Title: "An RNA foundation model enables discovery of disease mechanisms and candidate therapeutics"
    URL: https://www.biorxiv.org/content/10.1101/2023.09.20.558508v1
    AuthorName: Albi Celaj, Alice Jiexin Gao, Tammy T.Y. Lau, Erle M. Holgersen, Alston Lo, Varun Lodaya, Christopher B. Cole, Robert E. Denroche, Carl Spickett, Omar Wagih, Pedro O. Pinheiro, Parth Vora, Pedrum Mohammadi-Shemirani, Steve Chan, Zach Nussbaum, Xi Zhang, Helen Zhu, Easwaran Ramamurthy, Bhargav Kanuparthi, Michael Iacocca, Diane Ly, Ken Kron, Marta Verby, Kahlin Cheung-Ong, Zvi Shalev, Brandon Vaz, Sakshi Bhargava, Farhan Yusuf, Sharon Samuel, Sabriyeh Alibai, Zahra Baghestani, Xinwen He, Kirsten Krastel, Oladipo Oladapo, Amrudha Mohan, Arathi Shanavas, Magdalena Bugno, Jovanka Bogojeski, Frank Schmitges, Carolyn Kim, Solomon Grant, Rachana Jayaraman, Tehmina Masud, Amit Deshwar, Shreshth Gandhi, Brendan J. Frey
    AuthorURL: https://www.biorxiv.org/content/10.1101/2023.09.20.558508v1.article-info