A list of collaborative computational projects supported by CZI!
Here is a sample template you can copy and paste to add your project:
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|---|---|
| [name](link to repo) | description of the project | Jeremy Freeman, PhD @ CZI Science |
| [another project name](link to repo) | description of the project | Joe Hand and Danielle Robinson, PhD @ CS&S |
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|---|---|
| SingleCellExperiment | R container for storing data from single-cell experiments | Davide Risso @ Weill Cornell Medicine and Aaron Lun @ CRUK Camrbidge Institute |
| beachmat | Provides a consistent R/C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices. | Aaron Lun @ CRUK Camrbidge Institute |
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
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| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
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| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
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| Tybalt | Variational Autoencoder for Gene Expression (Paper) | Greg Way, Qiwen Hu, and Casey Greene @Greenelab @Penn |
| PHATE | Visualizing high-dimensional data (Paper) | Kevin Moon, David van Dijk, and Smita Krishnaswamy @KrishnaswamyLab @Yale |
| CoGAPS | Bayesian Non-Negative Matrix Factorization | Elana Fertig, Genevieve Stein-O'Brien, and Tom Sherman @FertigLab |
| alevin | Barcode correction, UMI deduplication and gene quantification for droplet-based scRNA-seq | Avi Srivastava, Tom Smith, Ian Sudbery and Rob Patro @COMBINE-lab |
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|---|---|
| CellBench | Benchmark data for scRNA-seq | Matt Ritchie, Luyi Tian @LuyiTian, WEHI |
| mixOmics paper | A suite of latent component based methods encompassing different data integration frameworks (cross-platform, multi-omics) and feature selection | Kim-Anh Le Cao@lecaolab, University of Melbourne |
| The Rosetta project: translating data across single-cell technologies to define human cell types | Use parallel population-level mRNA & morphology data to uncover relationships between the two data types; test predictivity at a single-cell level | Anne Carpenter, Juan Caicedo @CarpenterLab, Broad Institute |
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|---|---|
| IA-SVA | Iteratively Adjusted Surrogate Variable Analyses (Paper) | Donghyung Lee @LeeLab, Anthony Cheng, Mohan Bolisetty, Duygu Ucar @UcarLab @JAX |
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|---|---|
| ASAP | Automated Single-cell Analysis Pipeline (Web portal) (Paper) | Vincent Gardeux, Fabrice David, and Bart Deplancke @DeplanckeLab @EPFL |
| Xena | Web-browser based integrative functional genomics data visualization (Web site) | Brian Craft, Mary Goldman, Jing Zhu @ucscXena @UCSCXena |
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|---|---|
| ADAM | ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. | Michael Heuer, Anthony Joseph, UC Berkeley; Ryan Williams, Uri Laserson, Icahn School of Medicine at Mount Sinai. |
| TITLE | DESCRIPTION | PEOPLE & AFFILIATIONS |
|---|---|---|
| STREAM | STREAM is an interactive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data (and soon scMethyl-Data!) Paper. We also provide an interactive website to compute and visualize trajectories and a database of precomputed trajectories: http://stream.pinellolab.org | H Chen, L Albergante, JY Hsu, CA Lareau, GL Bosco, J Guan, S Zhou, AN Gorban, DE Bauer, MJ Aryee, DM Langenau, A Zinovyev, JD Buenrostro, GC Yuan, L Pinello @PinelloLab |
| traj-formats | Traj-formats contains json-schema specifications for trajectory information. | Collaborative effort from the trajectory community. Maintained by the @Stuart Lab at UCSC |