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Top 57 single-cell open source projects

scPower
Experimental design framework for scRNAseq population studies (eQTL and DE)
velodyn
Dynamical systems methods for RNA velocity analysis
switchde
Inference of switch-like differential expression along single-cell trajectories
netSmooth
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
babel
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
cellSNP
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
dbMAP
A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.
kmer-homology-paper
Manuscript for functional prediction of transcriptomic “dark matter” across species
EWCE
Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
alevin-fry
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
scABC
No description or website provided.
EDS
💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format
MERINGUE
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
iDEA
Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
scDblFinder
Methods for detecting doublets in single-cell sequencing data
mgatk
mgatk: mitochondrial genome analysis toolkit
OrchestratingSingleCellAnalysis-release
An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.
Pando
Multiome GRN inference.
crop-seq
Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
gchromVAR
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
cellrangerRkit
Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
cna
Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
kallistobustools
kallisto | bustools workflow for pre-processing single-cell RNA-seq data
SCopeLoomR
R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
VoxHunt
VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
GLUE
Graph-linked unified embedding for single-cell multi-omics data integration
SCOPE-tools
Single-Cell Omics Preparation Entity Tools
cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells
sinto
Tools for single-cell data processing
anndata2ri
Convert between AnnData and SingleCellExperiment
Nebulosa
R package to visualize gene expression data based on weighted kernel density estimation
trVAE
Conditional out-of-distribution prediction
CITE-seq-Count
A tool that allows to get UMI counts from a single cell protein assay
SCICoNE
Single-cell copy number calling and event history reconstruction.
NGS
Next-Gen Sequencing tools from the Horvath Lab
dyngen
Simulating single-cell data using gene regulatory networks 📠
scAlign
A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
scATAC-pro
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
ExpressionMatrix2
Software for exploration of gene expression data from single-cell RNA sequencing.
CrossTalkeR
R package to do the Ligand Receptor Analysis Visualization
1-57 of 57 single-cell projects