From 44b12a97901f3d7de3f66d6355169023e80dfd56 Mon Sep 17 00:00:00 2001 From: Ben Hitz Date: Thu, 11 Sep 2025 16:28:53 -0700 Subject: [PATCH] add igvf-consortium yaml --- datasets/igvf-consortium.yaml | 48 +++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 datasets/igvf-consortium.yaml diff --git a/datasets/igvf-consortium.yaml b/datasets/igvf-consortium.yaml new file mode 100644 index 000000000..aa38ad8ec --- /dev/null +++ b/datasets/igvf-consortium.yaml @@ -0,0 +1,48 @@ +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