Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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Updated
Mar 27, 2024
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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.
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
A single-cell RNAseq pipeline for 10X genomics data
R toolkit for the analysis of single-cell chromatin data
RNA velocity estimation in Python
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
R package for integrating and analyzing multiple single-cell datasets
Table of software for the analysis of single-cell RNA-seq data.
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
Deep neural networks for predicting CpG methylation
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
R package for analyzing single-cell RNA-seq data
A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
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