cole-trapnell-lab / monocle3
☆375Updated 2 months ago
Alternatives and similar repositories for monocle3:
Users that are interested in monocle3 are comparing it to the libraries listed below
- R package for detecting doublets in single-cell RNA sequencing data☆452Updated 2 weeks ago
- Community-provided extensions to Seurat☆328Updated 4 months ago
- Inferring CNV from Single-Cell RNA-Seq☆601Updated 2 months ago
- NicheNet: predict active ligand-target links between interacting cells☆526Updated last month
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆408Updated last month
- R toolkit for the analysis of single-cell chromatin data☆360Updated 2 months ago
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆469Updated 10 months ago
- A package to help convert different single-cell data formats to each other☆416Updated last year
- ☆353Updated 3 years ago
- High dimensional weighted gene co-expression network analysis☆388Updated this week
- R package for integrating and analyzing multiple single-cell datasets☆407Updated 2 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆559Updated 4 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆370Updated 3 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆318Updated 8 months ago
- ☆257Updated 4 months ago
- A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…☆482Updated 2 months ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆292Updated 4 years ago
- A toolkit for single-cell immune profiling☆328Updated last week
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆221Updated 3 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆268Updated 2 years ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆377Updated 2 months ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆489Updated 11 months ago
- Interpretation of cell states using reference single-cell maps☆268Updated last month
- Analysis Pipeline for Single Cell ATAC-seq☆314Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆362Updated 4 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆438Updated last year
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆347Updated 10 months ago
- ☆284Updated 2 years ago
- RNA Velocity generalized through dynamical modeling☆433Updated last month
- tools and notes for spatial omics☆280Updated last month