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48 changes: 48 additions & 0 deletions datasets/igvf-consortium.yaml
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Name: The Impact of Variation on Function Consortium (IGVF)
Description: |
The IGVF (Impact of Genomic Variation on Function) Consortium aims to understand how genomic variation affects genome function,
which in turn impacts phenotype. The NHGRI is funding this collaborative program that brings together teams of investigators who
will use state-of-the-art experimental and computational approaches to model, predict, characterize and map genome function, how
genome function shapes phenotype, and how these processes are affected by genomic variation. These joint efforts will produce a
catalog of the impact of genomic variants on genome function and phenotypes.
The Data Corpus consists of single-cell Genomics experiments (both single modal, and multimodal, typically snRNA-seq and snATAC-seq),
Characterization experiments using Massively Parallel Reporter Assays (MPRAs) and CRISPR-screens along with a variety of protein mutatation
assays, and Predictive Models.
There are a huge variety of files in IGVF that are stored in the AWS OpenData Set so we recommend using the [metadata file]() or browsing the [IGVF Data Portal](https://data.igvf.org)
Contact: igvf-portal-help@lists.stanford.edu
ManagedBy: IGVF Data Administration and Coordination Center at Stanford University
Documentation: https://data.igvf.org/general-help
UpdateFrequency: Daily
Tags:
- aws-pds
- biology
- bioinformatics
- genetic
- genomic
- life sciences
License: E[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) You are free to share abnd adapt tgus data with proper attribution.
Resources:
- Description: Released and Archived IGVF Data Files
ARN: arn:aws:s3:::igvf-public
Region: us-west-2
Type: S3 Bucket
DataAtWork:
Tutorials:
- Title:Load AnnData files from IGVF into scanpy and view the UMAPs
URL: https://github.com/IGVF-DACC/igvf-data-usage-examples/blob/master/igvf-scanpy.ipynb
AuthorName: Ben Hitz
AuthorURL: https://github.com/hitz
- Title: Ingesting IGVF Data into TileDB with S3 backend
URL: https://github.com/IGVF-DACC/igvf-data-usage-examples/blob/master/ingest_igvf_h5ad_data_to_anndata_and_tiledb.ipynb
AuthorName: Otto Jolanki
AuthorURL: https://github.com/ottojolanki
Tools & Applications:
- Title: The IGVF Catalog
URL: https://catalog.igvf.org
AuthorName: The IGVF Consortium
AuthorURL: www.igvf.org
Publications:
- Title: Deciphering the impact of genomic variation on function
URL: https://www-nature-com.stanford.idm.oclc.org/articles/s41586-024-07510-0
AuthorName: Jesse M. Engreitz and The IGVF Consortium
AuthorURL: https://orcid.org/0000-0002-5754-1719