single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Bayesian haplotype-based mutation calling

R package for integrating and analyzing multiple single-cell datasets

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

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

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.

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

R package for analyzing single-cell RNA-seq data

Single cell perturbation prediction

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Collection of public scRNA-Seq datasets used by our group

Deep neural networks for predicting CpG methylation

R toolkit for the analysis of single-cell chromatin data

Query to reference mapping for single-cell genomics

RNA velocity estimation in Python

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering

A software package for analyzing snapshots of developmental processes

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

Seurat meets tidyverse. The best of both worlds.

Content for the OSCA Book.

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

Convert between AnnData and SingleCellExperiment

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍