Yosef Lab

VISION

Signature Analysis and Visualization for Single-Cell RNA-seq

Compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes

Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

Hotspot

scone

scib-metrics

Accelerated, Python-only, single-cell integration benchmarking metrics

velovi

mrvi_archive

Multi-resolution Variational Inference

PopV

mrvi

Multi-resolution Variational Inference

scvi-criticism

Evaluation metrics for scvi-tools models

theoretical_lineage_tracing_reproducibility

yoseflab.github.io

velovi_reproducibility

VIVS

Calibrated Identification of Feature Dependencies in Single-cell Multiomics

CZI-Immuneaging

scvi-hub-references

Code for the pre-trained reference models uploaded to scvi-hub on HuggingFace

scvi-tools-docker

Docker images for scvi-tools

spatial-scvi

Deep probabilistic analysis of single-cell omics data

Thymus_CITE-seq

treedata

anndata with trees

visionpy

Functional interpretation of single cell similarity maps

census-scvi

criticism-tutorials

Notebooks used in scvi-criticism tutorials

destvi_utils

Utilities for downstream analysis of destVI

embedding-scvi

popv-reproducibility

Reproducibility for popV

pycea

scverse lineage tracing analysis toolkit

scvi-hub-models

Reproducibility workflows for pre-trained scvi-tools models on Hugging Face

scvi-hub-reproducibility

Reproducibility of results/figures from scvi-hub paper