bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

(2021) Pablo Moreno et al.   NATURE METHODS

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

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

(2018) Swati Parekh et al.   GigaScience

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS