Describes a platform for 3D in situ transcriptomics, enabled by DNA library preparation/sequencing and novel hydrogel-tissue chemistry. STARmap can map 10s-1000s of RNAs simultaneously in millimetre-scale volumes. This software has been tested for the study of molecularly-defined cell types and activity-regulated gene expression in mouse cortex and was able to be adapted to larger 3D tissues blocks to apprehend short- and long- range spatial organization of cortical neurons on a specific volumetric scale.
Allows comparative analysis of single-cell RNA-seq data. scQuery is a web application that supports the analysis of new, large scale single cell RNA (scRNA)-seq datasets. It includes features for processing all scRNA-seq experiments in public databases and for associating different profiles with cell type based on a constrained ontology. It also aligns the raw read data, assigns them to a pre-defined set of genes, and quantifies their expression.
Provides a stochastic gene expression model that allows for transcriptional switching between two states. This package implements a two-state stochastic switch model for the population of mRNA molecules in single cells, where transcription in the so called OFF state is less active than in the ON state, but may occur at a positive rate. This approach can serve for studying transcription in single cells from the kind of data arising in flow cytometry experiments.
Provides an interface for data access from R matrix representations. Beachmat serves for the implementation of computationally intensive algorithms in C++ that can be immediately applied to a wide range of R matrix classes. It allows researchers to investigate a large single-cell RNA sequencing (scRNA-seq) data set. This tool is useful for the study of high-throughput biological data stored in large matrices.
Evaluates and compares two or more single cell RNA-Seq samples. ClusterMap proceeds first by exploiting the marker genes for each sub-group of each sample as the basic input to perform the matching. It then visualizes the matching results through several views. Ultimately, this software defines the property modifications across samples for each matched group.
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