Yosef Lab (@YosefLab)
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Top repositories

1

VISION

Signature Analysis and Visualization for Single-Cell RNA-seq
R
152
star
2

Compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
Python
92
star
3

Hotspot

Python
83
star
4

Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
Python
76
star
5

scone

R
53
star
6

scib-metrics

Accelerated, Python-only, single-cell integration benchmarking metrics
Python
45
star
7

ImpulseDE2

R
37
star
8

velovi

Python
36
star
9

FastProject

Dimensionality reduction for single cell RNA-seq data
Python
35
star
10

SymSim

R
23
star
11

PopV

Python
23
star
12

mrvi_archive

Multi-resolution Variational Inference
Python
22
star
13

totalVI_reproducibility

Jupyter Notebook
15
star
14

TRAPeS

TCR Reconstruction Algorithm for Paired-End Single cell
Python
14
star
15

LineagePulse

Differential expression analysis for single-cell RNA-seq data
R
12
star
16

compassR

An R library for conducting analyses on COMPASS data.
R
12
star
17

MPRAnalyze

Analyse enhancer strength based on MPRA experiments.
R
11
star
18

epitome

Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
Python
10
star
19

ImpulseDE

ImpulseDE
R
6
star
20

scRAD

Single-Cell Reproducibility Across Donors
R
5
star
21

BRAPeS

BCR reconstruction from short single cell RNA-seq
Makefile
4
star
22

scvi-criticism

Evaluation metrics for scvi-tools models
Python
4
star
23

Rline

R wrapper around the LINE algorithm for network embedding
C++
4
star
24

mrvi

Multi-resolution Variational Inference
Python
4
star
25

UMIpipe

A pipeline for processing UMI RNAseq data
Jupyter Notebook
3
star
26

yoseflab.github.io

JavaScript
3
star
27

scVI-data

datasets for scVI
3
star
28

theoretical_lineage_tracing_reproducibility

Jupyter Notebook
3
star
29

temporal_condition_shortest_walk

Python
2
star
30

velovi_reproducibility

Jupyter Notebook
2
star
31

condition_connectivity_problems

Algorithms for connectivity problems in condition-varying protein networks
Python
2
star
32

VIVS

Calibrated Identification of Feature Dependencies in Single-cell Multiomics
Python
2
star
33

Thymus_CITE-seq

Jupyter Notebook
2
star
34

TcellSelectionTiming

HTML
1
star
35

scvi-tools-reproducibility

Reproducibility of results/figures from scvi-tools paper
HTML
1
star
36

treedata

anndata with trees
Python
1
star
37

visionpy

Functional interpretation of single cell similarity maps
JavaScript
1
star
38

scvi-hub-references

Code for the pre-trained reference models uploaded to scvi-hub on HuggingFace
Python
1
star
39

scvi-tools-docker

Docker images for scvi-tools
Dockerfile
1
star
40

CZI-Immuneaging

Jupyter Notebook
1
star