jingchunzhu / projects

a list of all projects

Computational tools for the Human Cell Atlas

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

Projects

Bioconductor

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

Cell Type

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS

Cell State

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS

Compression

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS

Imaging

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS

Latent Spaces

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS
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

Manifold Alignment

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS

Multiomics

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS

Population Variation

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS
IA-SVA	Iteratively Adjusted Surrogate Variable Analyses (Paper)	Donghyung Lee @LeeLab, Anthony Cheng, Mohan Bolisetty, Duygu Ucar @UcarLab @JAX

Portals

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS
ASAP	Automated Single-cell Analysis Pipeline (Web portal) (Paper)	Vincent Gardeux, Fabrice David, and Bart Deplancke @DeplanckeLab @EPFL

Scale

TITLE	DESCRIPTION	PEOPLE & AFFILIATIONS

Trajectories

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