single-cell
There are 852 repositories under single-cell topic.
seandavi/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
theislab/single-cell-best-practices
https://www.sc-best-practices.org
COMBINE-lab/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
mdozmorov/scRNA-seq_notes
A list of scRNA-seq analysis tools
flowhub-team/awesome-omics
A collection of awesome things regarding all omics.
Starlitnightly/omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
KrishnaswamyLab/PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
aertslab/pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
agitter/single-cell-pseudotime
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
welch-lab/liger
R package for integrating and analyzing multiple single-cell datasets
gao-lab/GLUE
Graph-linked unified embedding for single-cell multi-omics data integration
smorabit/hdWGCNA
High dimensional weighted gene co-expression network analysis
OmicsML/dance
DANCE: a deep learning library and benchmark platform for single-cell analysis
theislab/scarches
Reference mapping for single-cell genomics
stuart-lab/signac
R toolkit for the analysis of single-cell chromatin data
milaboratory/mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Teichlab/celltypist
A tool for semi-automatic cell type classification
immunomind/immunarch
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
scRNA-tools/scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
luntergroup/octopus
Bayesian haplotype-based mutation calling
theislab/scgen
Single cell perturbation prediction
genecell/single-cell-papers-with-code
Papers with code for single cell related papers
sdparekh/zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
samuel-marsh/scCustomize
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
iSEE/iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
nf-core/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
ZJUFanLab/scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
kharchenkolab/pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
digitalcytometry/ecotyper
EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
dtm2451/dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
vitessce/vitessce
Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
saezlab/liana-py
LIANA+: an all-in-one framework for cell-cell communication
saezlab/decoupler-py
Python package to perform enrichment analysis from omics data.