CELLxGENE Discover Census

Tutorials

• Computing on the cell by gene matrix using online (incremental) algorithms by Biohub
  
  
• Experimental Highly Variable Genes API by Biohub
  
  
• Exploring all data from a tissue by Biohub
  
  
• Exploring pre-calculated summary cell counts by Biohub
  
  
• Exploring the Census Datasets table by Biohub
  
  
• Genes measured in each cell (dataset presence matrix) by Biohub
  
  
• Integrating multi-dataset slices of data by Biohub
  
  
• Learning about the CELLxGENE Census by Biohub
  
  
• Normalizing full-length gene sequencing data by Biohub
  
  
• Out-of-core (incremental) mean and variance calculation by Biohub
  
  
• Querying and fetching the single-cell data and cell/gene metadata. by Biohub
  
  
• Querying data using the gget cellxgene module by Biohub
  
  
• Summarizing cell and gene metadata by Biohub
  
  
• Training a PyTorch Model by Biohub
  
  
• Understanding and filtering out duplicate cells by Biohub
  
  

Tools & Applications

• Census Python API by Biohub
  
• Census R API by Biohub
  

Publications

• CELLxGENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data by Biohub Single-Cell Biology et al.
  
• scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI. by Haotian Cui, et al.
  

Refgenie reference genome assets

Tutorials

• Basic Refgenie tutorial by Nathan Sheffield
  

Tools & Applications

• Pipeline for ATAC-seq data analysis by Jason Smith and Nathan Sheffield
  
• Pipeline for PRO-seq data analysis by Jason Smith and Nathan Sheffield
  

Publications

• Refgenie: a reference genome resource manager by Michał Stolarczyk, Vincent P Reuter, Jason P Smith, Neal E Magee, Nathan C Sheffield
  

Human and Mammalian Brain Atlas

Tutorials

• Human-Mammalian Brain - Basal Ganglia - Data by Allen Institute for Brain Science
  
• Human-Mammalian Brain - CCF Book by Allen Institute for Brain Science
  

Tools & Applications

• HMBA Basal Ganglia resources in Brain Knowledge Platform's Data Catalog by Allen Institute for Brain Science
  

Human Cell Atlas

Publications

• The Human Cell Atlas from a cell census to a unified foundation model by Jennifer E. Rood, Samantha Wynne, Lucia Robson, Anna Hupalowska, John Randell, Sarah A. Teichmann & Aviv Regev
  
• The Human Cell Atlas White Paper by Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, Gary Bader, Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau, Peter Campbell, Mary Carmichael, Piero Carninci, Leslie Castelo-Soccio, Menna Clatworthy, Hans Clevers, Christian Conrad, Roland Eils, Jeremy Freeman, Lars Fugger, Berthold Goettgens, Daniel Graham, Anna Greka, Nir Hacohen, Muzlifah Haniffa, Ingo Helbig, Robert Heuckeroth, Sekar Kathiresan, Seung Kim, Allon Klein, Bartha Knoppers, Arnold Kriegstein, Eric Lander, Jane Lee, Ed Lein, Sten Linnarsson, Evan Macosko, Sonya MacParland, Robert Majovski, Partha Majumder, John Marioni, Ian McGilvray, Miriam Merad, Musa Mhlanga, Shalin Naik, Martijn Nawijn, Garry Nolan, Benedict Paten, Dana Pe'er, Anthony Philippakis, Chris Ponting, Steve Quake, Jayaraj Rajagopal, Nikolaus Rajewsky, Wolf Reik, Jennifer Rood, Kourosh Saeb-Parsy, Herbert Schiller, Steve Scott, Alex Shalek, Ehud Shapiro, Jay Shin, Kenneth Skeldon, Michael Stratton, Jenna Streicher, Henk Stunnenberg, Kai Tan, Deanne Taylor, Adrian Thorogood, Ludovic Vallier, Alexander van Oudenaarden, Fiona Watt, Wilko Weicher, Jonathan Weissman, Andrew Wells, Barbara Wold, Ramnik Xavier, Xiaowei Zhuang, Human Cell Atlas Organizing Committee
  
• The Human Cell Atlas: towards a first draft atlas by Various authors
  
• The Human Cell Atlas: towards a first draft atlas by Various authors
  
• The network effect: studying COVID-19 pathology with the Human Cell Atlas by Sarah Teichmann, Aviv Regev
  

Tabula Sapiens

Publications

• Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues by The Tabula Sapiens Consortium, Stephen R Quake
  
• The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans by The Tabula Sapiens Consortium
  

LongBench - cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

Tutorials

• Benchmarking long-read DE gene and transcript analysis with edgeR by Yupei You
  

Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD)

Tools & Applications

• Seattle Alzheimer’s Disease Brain Cell Atlas by Lein, E et al.
  

Single-Cell Atlas of Human Blood During Healthy Aging

Publications

• Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB−CD8+ memory T cells and accumulation of type 2 memory T cells by Terekhova M, Swain A, Bohacova P, Aladyeva E, Arthur L, et al
  

Tabula Muris Senis

Tutorials

• Fast queries of scRNAseq datasets with Amazon Athena by Andrew Ang, James Golden, Lisa McFerrin, and Lee Pang
  Amazon AthenaAWS Glue