Dimension reduction software tools | Single-cell RNA sequencing data analysis

Offers a method for dimensionality reduction based on parametrization. t-SNE parametrizes the non-linear mapping between the data space and the latent space by means of a feed-forward neural network. This software is implemented into seven different languages, and, additionally, as Barnes-Hut and parametric implementation. This tool is fitted for the visualization of high-dimensional datasets.

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).

Facilitates the analysis of cellular heterogeneity, the identification of cell types, and comparison of functional markers in response to perturbations, based on a versatile method. SPADE helps to organize high-dimensional cytometry data in an unsupervised manner, and to investigate natural and pathogenic cellular heterogeneity for biological insight. The SPADE algorithm consists of four components: (i) density-dependent downsampling, (ii) clustering, (iii) linking clusters with a minimum spanning tree, and (iv) upsampling to restore all cells in the final result. This modularized process allows more efficient sub-algorithms to replace the current components. In this sense, SPADE can be viewed as a framework for cytometric data analysis and visualization that has the capacity to be evolved and adapted.

Allows users to analyze single-cell gene expression experiments. Monocle can realize differential expression analysis, clustering, visualization, and other useful tasks on single-cell expression data. The software enjoins individual cells according to a defined progress through a biological process, without knowing ahead of time which genes define progress through that process. It is designed to work with RNA-Seq and quantitative polymerase chain reaction (qPCR) data, and implements Census and BEAM tools.

Allows studying of spatial patterning of gene expression at the single-cell level. Seurat is an R package that enables quality control (QC), analysis, and exploration of single cell RNA-seq data. The software includes three computational methods: (1) unsupervised clustering and discovery of cell types and states, (2) spatial reconstruction of single cell data, and (3) integrated analysis of single cell RNA-seq across conditions, technologies, and species. It can also localize rare subpopulations, and map both spatially restricted and scattered groups.

Contains useful tools for the analysis of single-cell gene expression data using the statistical software R. scater places an emphasis on tools for quality control, visualisation and pre-processing of data before further downstream analysis. scater enables the following: (i) automated computation of QC metrics; (ii) transcript quantification from read data with pseudo-alignment; (iii) data format standardisation; (iv) rich visualisations for exploratory analysis; (v) seamless integration into the Bioconductor universe; (vi) simple normalisation methods.

An ultrafast algorithm which uses a novel yet very simple "implicit imputation" approach to alleviate the impact of dropouts in single cell RNA-seq (scRNA-seq) data in a principled manner. Using a range of simulated and real data, we have shown that CIDR outperforms the state-of-the-art methods, namely t-SNE, ZIFA and RaceID, by at least 50% in terms of clustering accuracy, and typically completes within seconds for processing a dataset of hundreds of cells. We believe that single-cell mRNA sequencing in combination with the RaceID algorithm is a powerful tool to unravel heterogeneity of rare cell types in both healthy and diseased organs.