scanpy

Label: Scanpy
Package: scanpy
Tool Type: Python
Title: Single-Cell Analysis in Python
Description: Scanpy is a scalable toolkit for analyzing single-cell RNA-seq data. It includes preprocessing, visualization, clustering, trajectory inference, and differential expression testing. ASAP uses Scanpy for normalization, highly variable gene selection, PCA, neighborhood graphs, Leiden/Louvain clustering, t-SNE, and UMAP. Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology 19:15 (2018). doi:10.1186/s13059-017-1382-0