Awesome Single CellCommunity-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
scPowerExperimental design framework for scRNAseq population studies (eQTL and DE)
velodynDynamical systems methods for RNA velocity analysis
switchdeInference of switch-like differential expression along single-cell trajectories
fastq utilsValidation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
netSmoothnetSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
babelDeep learning model for single-cell inference of multi-omic profiles from a single input modality.
scarchesReference mapping for single-cell genomics
cellSNPPileup biallelic SNPs from single-cell and bulk RNA-seq data
dbMAPA 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-paperManuscript for functional prediction of transcriptomic “dark matter” across species
EWCEExpression 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.
scABCNo description or website provided.
EDS💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format
SpiceMixspatial transcriptome, single cell
MERINGUEcharacterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
iDEADifferential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
scDblFinderMethods for detecting doublets in single-cell sequencing data
mgatkmgatk: mitochondrial genome analysis toolkit
PandoMultiome GRN inference.
crop-seqData analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
gchromVARCell type specific enrichments using finemapped variants and quantitative epigenetic data
scCATCHAutomatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
cellrangerRkitNon-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
cnaCovarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
immunarch🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
GCModellerGCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language
celltypistA tool for semi-automatic cell type annotation
kallistobustoolskallisto | bustools workflow for pre-processing single-cell RNA-seq data
SCopeLoomRR package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
VoxHuntVoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
GLUEGraph-linked unified embedding for single-cell multi-omics data integration
bapBead-based single-cell atac processing
cellsnp-liteEfficient genotyping bi-allelic SNPs on single cells
sintoTools for single-cell data processing
anndata2riConvert between AnnData and SingleCellExperiment
kanaSingle cell analysis in the browser
NebulosaR package to visualize gene expression data based on weighted kernel density estimation
trVAEConditional out-of-distribution prediction
CITE-seq-CountA tool that allows to get UMI counts from a single cell protein assay
SCICoNESingle-cell copy number calling and event history reconstruction.
NGSNext-Gen Sequencing tools from the Horvath Lab
dyngenSimulating single-cell data using gene regulatory networks 📠
scAlignA deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
SCopeFast visualization tool for large-scale and high dimensional single-cell data
scATAC-proA comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
ExpressionMatrix2Software for exploration of gene expression data from single-cell RNA sequencing.
CrossTalkeRR package to do the Ligand Receptor Analysis Visualization
cardelinoClone identification from single-cell data