An integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large ensembles of single-cell RNA-seq datasets. SCell is open source, and implemented with an intuitive graphical interface.
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.
Allows to perform several low-level analyses on of single-cell RNA-seq data. Scran is a package that provides functions to normalize cell-specific biases, assign cell cycle phase, and detect highly variable and significantly correlated genes.
Allows quality control (QC) and analysis components of parallel single cell transcriptome and epigenome data. Dr.seq is a quality control (QC) and analysis pipeline that provides both multifaceted QC reports and cell clustering results. Parallel single cell transcriptome data generated by different technologies can be transformed to the standard input with contained functions. Using relevant commands, the software can also be used to report quality measurements based on four aspects and can generate detailed analysis results for scATAC-seq and Drop-ChIP datasets.
Allows users to remove batch effects. BBKNN offers an alignment approach suitable for a conjunctional use with the Scanpy software. This program can generate neighbor graphs as well as uniform manifold approximation and projection (UMAP) visualization. It also includes features to calculate approximate nearest neighbors. It generates files that can be used for further analysis containing clustering and pseudotime inference.
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