#single-cell (30 Repositories)
Ranked open-source repositories tagged with #single-cell, scored by pull request acceptance likelihood and maintainer engagement velocity.
49.6%
65.0h
30 repositories tagged #single-cell
omicverse/omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
scverse/rapids-singlecell
rapids-singlecell: GPU-accelerated framework for scRNA analysis
theislab/anndata2ri
Convert between AnnData and SingleCellExperiment
scverse/pertpy
Single-cell perturbation analysis
COMBINE-lab/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.
NygenAnalytics/scarf
Memory-efficient single-cell analysis in Python. Stream RNA, ATAC, CITE-seq and multi-omics from local or remote Zarr stores, from laptop to atlas scale, with reusable fingerprinted results.
scverse/decoupler
Python package to perform enrichment analysis from omics data.
theislab/moscot
Multi-omic single-cell optimal transport tools
milaboratory/mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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
scverse/liana-py
LIANA+: an all-in-one framework for cell-cell communication
cafferychen777/mLLMCelltype
Cell type annotation for single-cell RNA-seq using multi-LLM consensus
stuart-lab/signac
R toolkit for the analysis of single-cell chromatin data
iSEE/iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
TianGzlab/OmicsClaw
Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper.
scRNA-tools/scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
digitalcytometry/ecotyper
EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
lilab-bcb/cirrocumulus
Bring your single-cell data to life
ZJUFanLab/scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
smorabit/hdWGCNA
High dimensional weighted gene co-expression network analysis
sdparekh/zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
dtm2451/dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
welch-lab/liger
R package for integrating and analyzing multiple single-cell datasets
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
enblacar/SCpubr
Generate high quality, publication ready visualizations for single cell transcriptomics data.
gao-lab/GLUE
Graph-linked unified embedding for single-cell multi-omics data integration
luntergroup/octopus
Bayesian haplotype-based mutation calling
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.