dylkot / cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
☆302Updated 5 months ago
Alternatives and similar repositories for cNMF:
Users that are interested in cNMF are comparing it to the libraries listed below
- A package to help convert different single-cell data formats to each other☆405Updated 11 months ago
- A tool for semi-automatic cell type classification☆333Updated last month
- Benchmarking analysis of data integration tools☆331Updated last month
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆306Updated 6 months ago
- A novel machine learning pipeline to analyse spatial transcriptomics data☆207Updated 8 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆335Updated 8 months ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆222Updated last year
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆346Updated 2 months ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆201Updated 3 weeks ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆264Updated 2 years ago
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆242Updated last week
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆362Updated last month
- This is the alpha version of the CellOracle package☆331Updated last month
- Scanpy Tutorials.☆198Updated this week
- A toolkit of spatial transcriptomic analysis.☆216Updated this week
- A toolkit for single-cell immune profiling☆325Updated this week
- ☆353Updated 3 years ago
- High dimensional weighted gene co-expression network analysis☆375Updated 2 weeks ago
- NicheNet: predict active ligand-target links between interacting cells☆513Updated 5 months ago
- Reference mapping for single-cell genomics☆347Updated last month
- tools and notes for spatial omics☆265Updated 4 months ago
- Analysis Pipeline for Single Cell ATAC-seq☆310Updated last year
- A scalable SCENIC workflow for single-cell gene regulatory network analysis☆149Updated 2 years ago
- This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data☆121Updated last year
- ☆363Updated last month
- Spatial omics analysis toolbox☆278Updated last week
- Interpretation of cell states using reference single-cell maps☆263Updated 2 months ago
- Differential expression analysis for single-cell RNA-seq data.☆196Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆353Updated 2 months ago
- EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.☆193Updated 10 months ago