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SPADE / Spanning tree Progression of Density normalized Events
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 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 orders individual cells according to 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 qPCR data, but could be used with other types as well. The tools Census and BEAM are implemented in Monocle.
A computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. TraCeR extracts TCR-derived sequencing reads for each cell by alignment against ‘combinatorial recombinomes’ comprising all possible combinations of V and J segments. Reads are then assembled into contiguous sequences that are analyzed to find full-length, recombined TCR sequences. Importantly, the reconstructed recombinant sequences typically contain nearly the complete length of the TCR V(D)J region and so allow high-confidence discrimination between closely related gene segments. Our method is sensitive, accurate and easy to adapt to any species for which annotated TCR gene sequences are available.
Offers a simple interface for creating complex simulations that are reproducible and well-documented. Splatter is an R package for reproducible and accurate simulation of single-cell RNA sequencing data. It enables researchers to quickly simulate scRNA-seq count data in a reproducible fashion and make comparisons between simulations and real data. This framework can empower researchers to rapidly and rigorously develop new scRNA-seq analysis methods, ultimately leading to new discoveries in cell biology.
MATCHER / Manifold Alignment To CHaracterize Experimental Relationships
Characterizes corresponding transcriptomic and epigenetic changes in embryonic stem cells (ESCs). MATCHER gives insight into the sequential changes of genomic information. It allows the use of both single cell gene expression and epigenetic data in the construction of cell trajectories. The tool can be useful for studying a variety of biological processes, such as differentiation, reprogramming, immune cell activation, and tumorigenesis.
TSCAN / Tools for Single Cell ANalysis
A software tool developed to better support in silico pseudo-time reconstruction in single-cell RNA-seq analysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods.
Eclair / Ensemble Cell Lineage Analysis with Improved Robustness
A computational method for the statistical inference of cell lineage relationships from single-cell gene expression data. ECLAIR uses an ensemble approach to improve the robustness of lineage predictions, and provides a quantitative estimate of the uncertainty of lineage branchings. We show that the application of ECLAIR to published datasets successfully reconstructs known lineage relationships and significantly improves the robustness of predictions. In conclusion, ECLAIR is a powerful bioinformatics tool for single-cell data analysis. It can be used for robust lineage reconstruction with quantitative estimate of prediction accuracy.
Preserves distinct structural properties of the data. dropClust uses Locality Sensitive Hashing (LSH), a logarithmic-time algorithm to determine approximate neighborhood for individual transcriptomes. It employs an exponential decay function to select higher number of expression profiles from clusters of relatively smaller sizes. This tool is able to detect principal components (PCs) with multi-modal distribution of the projected transcriptomes by using mixtures of Gaussians.
Simulates and evaluates differential expression from bulk and especially single-cell RNA-seq data. powsimR can not only estimate sample sizes necessary to achieve a certain power, but also informs about the power to detect differential expression (DE) in a data set at hand. This module integrates estimated and simulated expression differences to calculate marginal and conditional error matrices. To calculate these matrices, the user can specify nominal significance levels, methods for multiple testing correction and gene filtering schemes.
Models time series accounting for noise in the temporal dimension. This R package implements the DeLorean model to estimate pseudotimes for cell expression data. The DeLorean model uses a Gaussian process latent variable model to model uncertainty in the capture time of cross-sectional data. This method was specifically designed for single cell transcriptome experiments. It was fit to three separate datasets each using a different biological assay (microarrays, single cell nCounter and single cell RNA-seq) in three organisms (human, mouse and Arabidopsis).
ASAP / Automated Single-cell Analysis Pipeline
Aims at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment. ASAP combines a wide range of commonly used algorithms with sophisticated visualization tools. It allows researchers to interact with the data in a straightforward fashion and in real time.
A tool for uncovering high-dimensional structure in single-cell gene expression data. From a table of gene expression measurement for single-cells, SPRING is able to build a k-nearest neighbor (knn) graph and display the graph using a force-directed layout algorithm that renders a real-time simulation in an interactive viewing window. SPRING offers an open-ended data exploration, including interactive discovery of markers genes, genes expression comparison between different subpopulations and selection tools for isolating subpopulations of interest.
Produces tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. CellTree can infer complex underlying hierarchical structures in cell populations from expression data alone, and also provide biological backing for the model it creates. The package can provide reasonable default values for most of the parameters used by the model inference, visualisation and analysis algorithms, making it possible for an unfamiliar user of the software to quickly evaluate a new dataset in a few simple lines of R code.
Sake / Single-cell RNA-Seq Analysis and Klustering Evaluation
Assists in navigating through the expression profile. SAKE is an R package that uses non-negative matrix factorization (NMF) method for unsupervised clustering. It offers (i) quality controls modules to compare total sequenced reads to total gene transcripts detected, (ii) sample correlation heatmap plot, (iii) heatmap of sample assignment from NMF run, with dark red indicating high confidence in cluster assignments, and (iv) t-distributed stochastic neighbor embedding (t-SNE) plot to compare NMF assigned groups with t-SNE projections.
UNCURL / UNified CompUtational framework for scRNA-seq data processing and Learning
Allows unsupervised and semi-supervised learning using Single Cell RNA-Seq data. To operate these learning, UNCURL provides a method for standardizing any prior biological information including bulk RNA-seq data, microarray data or even information about individual marker gene expression to a form compatible with scRNA-Seq data. Additionally, this package allows the integration of prior information which leads to large improvements in accuracy.
Assists users in the estimation of velocity and the related data analysis. Velocyto is an analysis framework developed for the analysis of expression dynamics single cell RNA seq data. This analysis logic is implemented separately in R and python environments. This method consists of two main components: (i) a command line interface (CLI) used to run the pipeline that generates spliced/unspliced expression matrices and (ii) a library that includes functions to estimate RNA velocity from the data matrices.
SWNE / Similarity Weighted Nonnegative Embedding
Assists in visualizing high dimensional datasets. SWNE is based on a method that apprehends both the local and global structure of the data and enables relevant biological factors and genes to be embedded directly onto the visualization. By capturing global structure, this software finds differentiation trajectories and layer specific neuron structure that is not visible in other visualizations. It can also capture the layer specific structure of excitatory neurons.
ascend / Analysis of Single Cell Expression, Normalisation and Differential expression
Allows creation of workflow for the analysis of Single cell RNA sequencing (scRNA-seq) experiments. ascend can handle data generated from any single cell library preparation platform. It includes functions to leverage multiple CPUs, allowing most analyses to be performed on a standard desktop or laptop. In summary, this tool implements a state-of-the-art unsupervised clustering method and integrates established analysis techniques for normalization and differential gene expression.
SAUCIE / Sparse Autoencoder for Unsupervised Clustering, Imputation, and Embedding
Offers a method for handling and extracting structure from single-cell RNA-sequencing and CyTOF data. SAUCIE is a standalone software that provides a deep learning approach developed for the analysis of single-cell data from a cohort of patients. The application is based on different layers able to performs several tasks such as data imputation, clustering, batch correction or visualization. The approach is based on the autoencoder neural network framework for unsupervised learning.
Enables immersive visualization of single-cell data for hundreds of thousands of cells using a mobile-enabled web browser. starmap is an online application that combines the benefit of a three-dimensional scatter plot for exploring clustering structure and the benefit of star plots for multivariate visualization of an individual cell. Moreover, this tool is designed to allow production of 3D and virtual reality (VR) experiences, such as A-Frame and Three.js, which are cross-platform and can be adapted to computer screens and VR devices.
PIVOT / Platform for Interactive analysis and Visualization Of Transcriptomics data
Allows users to analyze and visualize RNA-Seq data. PIVOT furnishes four mains functionalities (i) a graphical interface that is able to wrap existing open source packages in a single user-interface (ii) multiple tools to manipulate datasets to perform derivation or normalization (iii) a way for allowing the compatibility between inputs and outputs from different analysis modules and, (iv) functions for automatically generate reports, publication-quality figures, and reproducible computations.
SCONE / Single-Cell Overview of Normalized Expression
Assists in implementing and assessing the performance of a range of normalization workflows. SCONE evaluates the performance of each workflow and ranks them by aggregating over a set of performance metrics. It is applicable to different single-cell RNASeq (scRNAseq) protocols including microfluidic, plate, and droplet, methods. It allows researchers to compare a set of default normalizations as well as to include user-defined normalization methods.
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.
Provides an easy-to-use and intuitive workflow for basic analysis of single-cell RNA-Seq data. hocuspocus combines custom functions with functions from available packages. Particular emphasis is placed on data presentation and visualization, with a variety of options for controlling the appearance of plots. Currently, tools include selection of important expressed genes based on variance and PCA, heatmaps with color bars, blot plots, 1D, 2D, and 3D PCA plots, clustering analysis, gap statistic calculation, and all of the temporal ordering and differential expression analysis tools from monocle.
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