single-cell-rna-seq

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

zhanghao-njmu/SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

cole-trapnell-lab/monocle3

theislab/cellrank

CellRank: dynamics from multi-view single-cell data

OmicsML/dance

DANCE: a deep learning library and benchmark platform for single-cell analysis

scRNA-tools/scRNA-tools

Table of software for the analysis of single-cell RNA-seq data.

xuranw/MuSiC

Multi-subject Single Cell Deconvolution

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.

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

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

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.

saezlab/liana-py

LIANA+: an all-in-one framework for cell-cell communication

kharchenkolab/numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

enblacar/SCpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.

quadbio/scRNAseq_analysis_vignette

Tutorial for scRNA-seq data analysis beginners using R

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

mojaveazure/seurat-disk

Interfaces for HDF5-based Single Cell File Formats

theislab/scCODA

A Bayesian model for compositional single-cell data analysis

pwwang/scplotter

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

saeyslab/multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

dynverse/dynmethods

A collection of 50+ trajectory inference methods within a common interface 📥📤

hemberg-lab/SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

tallulandrews/scRNASeqPipeline

martinjzhang/scDRS

Single-cell disease relevance score (scDRS)

satijalab/azimuth

A Shiny web app for mapping datasets using Seurat v4

rnabioco/clustifyr

Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets

tanaylab/metacell

Metacell - Single-cell mRNA Analysis

GregorySchwartz/too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.

yanwu2014/swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets