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FileSet
DSR254454
released
Annotation file set: List of genes differentially expressed among human samples from Joseph Wu Lab at Stanford. Single Cell Multiomics and Deep Learning of Human Cardiac and Peripheral Artery Tissues
Lab: Joseph Wu, Stanford
Project: community
FileSet
DSR901522
released
Annotation file set: List of genes expression levels among human samples from Joseph Wu Lab at Stanford. Single Cell Multiomics and Deep Learning of Human Cardiac and Peripheral Artery Tissues
Lab: Joseph Wu, Stanford
Project: community
Publication
released
A comparative atlas of single-cell chromatin accessibility in the human brain
Yang Eric Li, Sebastian Preissl, Michael Miller, et al.
Science. 2023-10-13;382(6667)
Publication
released
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes
Kristina M. Garske, Asha Kar, Caroline Comenho, et al.
Nat Commun. 2023-07-14;14(1):4214.
Publication
released
Three-dimensional chromatin organization in cardiac development and disease
Alessandro Bertero, Manuel Rosa-Garrido.
J Mol Cell Cardiol. 2020-11-24;151:89-105.
Publication
released
Lineage-specific differences and regulatory networks governing human chondrocyte development
Daniel Richard, Steven Pregizer, Divya Venkatasubramanian, et al.
Elife. 2023-03-15;15:12:e79925
Software
released
dreamlet — source
A open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster.
Software type: other
Software
released
Scanpy — source
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing.
Software
released
scE2G — source
A new family of classification models, scE2G, to predict enhancer-gene regulation.
Software type: other
Software
released
ArchR — source
ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available.
Software type: other
FileSet
DSR291812
released
Embeddings file set: Single-nucleus chromatin accessibility profiles quantified at consensus peak summits, with UMAP embeddings generated using Scanpy. (150bp +/- of the consensus peak summit).
Lab: Stephen Parker, UMich
Project: AMP
FileSet
DSR144369
released
Embeddings file set: Single-nucleus RNA-seq gene expression profiles after ambient RNA correction, with UMAP embeddings generated using Scanpy.
Lab: Stephen Parker, UMich
Project: AMP
Experiment
DSR682903
released
snATAC-seq of skeletal muscle tissue
Lab: Stephen Parker, UMich
Project: AMP
Publication
released
Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits
Sarah M Brotman, Anniina Oravilahti, Jonathan D Rosen, et al.
Diabetes. 2023-11-01;72(11):1707-1718.
Publication
released
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
Kevin W Currin, Hannah J Perrin, Gautam K Pandey, et al.
Genome Res. 2025-05-20;
- doi:10.1101/gr.279741.124
- PMID:40393811
Publication
released
An atlas of healthy and injured cell states and niches in the human kidney
Blue B. Lake, Rajasree Menon, Seth Winfree, et al.
Nature. 2023-07-19;619(7970):585-594.
URL: https://www.nature.com/articles/s41586-023-05769-3
Publication
released
A comprehensive spatio-cellular map of the human hypothalamus
John A. Tadross, Lukas Steuernagel, Georgina K. C. Dowsett, et al.
Nature. 2025-02-05;639(8055):708-716.
URL: https://www.nature.com/articles/s41586-024-08504-8
Publication
released
Single cell multiomics and 3D genome architecture reveal novel pathways of human heart failure
Yang Xie, Luca Tucciarone, Elie N Farah, et al.
medRxiv.
- doi:10.1101/2025.05.08.25327176
URL: https://www.medrxiv.org/content/10.1101/2025.05.08.25327176v1
Publication
released
A single-cell atlas of human and mouse white adipose tissue
Margo P. Emont, Christopher Jacobs, Adam L. Essene, et al.
Nature. 2022-03-16;603(7903):926-933.
URL: https://www.nature.com/articles/s41586-022-04518-2
Publication
released
Single cell multiomics reveals drivers of metabolic dysfunction-associated steatohepatitis
Weston Elison, Lei Chang, Yang Xie, et al.
medRxiv.
- doi:10.1101/2025.05.09.25327043
URL: https://www.medrxiv.org/content/10.1101/2025.05.09.25327043v1
FileSet
DSR445357
released
Embeddings file set: Integrate object with UMAP and RNA counts for FNIH multiome, CAREHF multiome, DPT and HiC.
Lab: Kyle Gaulton, UCSD
Project: AMP
FileSet
DSR871NXS
released
Annotation file set: Accessible chromatin annotation of each cell type cluster identified from snRNA+snATAC profiling of human skeletal muscle - type 2a muscle cell
Lab: Stephen Parker, UMich
Project: AMP
FileSet
DSR059OPJ
released
Annotation file set: Accessible chromatin annotation of each cell type cluster identified from snRNA+snATAC profiling of human skeletal muscle - type 2x muscle cell
Lab: Stephen Parker, UMich
Project: AMP
FileSet
DSR152USV
released
Annotation file set: Accessible chromatin annotation of each cell type cluster identified from snRNA+snATAC profiling of human skeletal muscle - type 1 muscle cell
Lab: Stephen Parker, UMich
Project: AMP
FileSet
DSR437GPK
released
Annotation file set: Accessible chromatin annotation of each cell type cluster identified from snRNA+snATAC profiling of human skeletal muscle - T cell
Lab: Stephen Parker, UMich
Project: AMP

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Showing 25 of 47282 results