single-cell-rna-seq
There are 387 repositories under single-cell-rna-seq topic.
satijalab/seurat
R toolkit for single cell genomics
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
COMBINE-lab/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
scverse/squidpy
Spatial Single Cell Analysis in Python
OmicsML/dance
DANCE: a deep learning library and benchmark platform for single-cell analysis
theislab/cellrank
CellRank: dynamics from multi-view single-cell data
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
scRNA-tools/scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
xuranw/MuSiC
Multi-subject Single Cell Deconvolution
kharchenkolab/pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
kharchenkolab/conos
R package for the joint analysis of multiple single-cell RNA-seq datasets
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.
theislab/diffxpy
Differential expression analysis for single-cell RNA-seq data.
dtm2451/dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
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.
stemangiola/tidyseurat
Seurat meets tidyverse. The best of both worlds.
pachterlab/kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
theislab/scCODA
A Bayesian model for compositional single-cell data analysis
mojaveazure/seurat-disk
Interfaces for HDF5-based Single Cell File Formats
enblacar/SCpubr
Generate high quality, publication ready visualizations for single cell transcriptomics data.
saezlab/liana-py
LIANA+: an all-in-one framework for cell-cell communication
quadbio/scRNAseq_analysis_vignette
Tutorial for scRNA-seq data analysis beginners using R
hemberg-lab/SC3
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
dynverse/dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
rnabioco/clustifyr
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
yanwu2014/swne
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
tanaylab/metacell
Metacell - Single-cell mRNA Analysis
GregorySchwartz/too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
satijalab/azimuth
A Shiny web app for mapping datasets using Seurat v4
ttgump/scDeepCluster
scDeepCluster for Single Cell RNA-seq data
JEFworks-Lab/HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
saeyslab/multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data