woolf-wu's Stars
saezlab/decoupler-py
Python package to perform enrichment analysis from omics data.
Danko-Lab/BayesPrism
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
bvieth/powsimR
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
saezlab/liana
LIANA: a LIgand-receptor ANalysis frAmework
IanevskiAleksandr/sc-type
plger/scDblFinder
Methods for detecting doublets in single-cell sequencing data
aristoteleo/dynamo-release
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
tanaylab/metacells
Metacells - Single-cell RNA Sequencing Analysis
dylkot/cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
broadinstitute/Tangram
Spatial alignment of single cell transcriptomic data.
neurorestore/Libra
BayraktarLab/cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
dynverse/dynverse
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
theislab/scvelo
RNA Velocity generalized through dynamical modeling
mossjacob/pyslingshot
Python implementation of the Slingshot pseudotime algorithm
broadinstitute/infercnv
Inferring CNV from Single-Cell RNA-Seq
jackbibby1/SCPA
R package for pathway analysis in scRNA-seq data
andreariba/DeepCycle
Cell cycle inference in single-cell RNA-seq
YosefLab/VISION
Signature Analysis and Visualization for Single-Cell RNA-seq
zqfang/GSEApy
Gene Set Enrichment Analysis in Python
milaboratory/mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
JCVenterInstitute/NSForest
A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing
morris-lab/CellOracle
This is the alpha version of the CellOracle package
niaid/dsb
Normalize CITEseq Data
dpeerlab/SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
Teichlab/celltypist
A tool for semi-automatic cell type classification
saeyslab/multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
theislab/cellrank
CellRank: dynamics from multi-view single-cell data
snap-stanford/GEARS
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations