List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Contributions welcome...
- clusterExperiment - [R] - Functions for running and comparing many different clusterings of single-cell sequencing data. Meant to work with SCONE and slingshot
- MAST - [R] - Model-based Analysis of Single-cell Transcriptomics (MAST) fits a two-part, generalized linear models that are specially adapted for bimodal and/or zero-inflated single cell gene expression data.
- Monocle - [R] - Differential expression and time-series analysis for single-cell RNA-Seq.
- SCONE - [R] - SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.
- SCOUP - [C++] - Uses probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation.
- sincell - [R] - Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework.
- slingshot - [R] - Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data.
- Aaron Lun's Single Cell workflow on Bioconductor - [R] - This article describes a computational workflow for basic analysis of scRNA-seq data using software packages from the open-source Bioconductor project.
- Bioconductor2016 Single-cell-RNA-sequencing workshop by Sandrine Dudoit lab - [R] - SCONE, clusterExperiment, and slingshot tutorial.
- BiomedCentral Single Cell Omics collectin - collection of papers describing techniques for single-cell analysis and protocols.
- Hemberg Lab scRNA-seq course materials