Assists users in analyzing next-generation sequencing (NGS) data. snakePipes provides DNA-mapping, ChIP-seq, ATAC-seq, RNA-seq, whole-genome bisulfite-seq (WGBS), HiC and single-cell RNA-seq workflows. It employs extensive quality-checks and produces reports that inform users about processing and analysis results. It provides workflows that allow processing and downstream analysis of data in an allele-specific manner.
Serves for pre-processing of UMI-based single-cell experiments. PiGx scRNA-seq enables integration and quality control (QC) of multiple single cell data sets. It is able to produce processed files for downstream analysis and interactive quality reports. This tool also includes features permitting researchers to construct the digital gene expression matrix and perform computation per sample and per cell statistics.
Performs guided single-cell RNA-seq data analysis and clustering. SeuratWizard is a web-based interactive application based on Seurat, an R package designed for quality control (QC), analysis and exploration of single cell RNA-seq data. It provides a graphic interface for researchers to upload, analyze, visualize, and explore their data. It includes various forms of visualizations for QC/filter, dimensionality reduction, clustering, and gene expression.
Defines a S4 class for storing data from single-cell experiments. SingleCellExperiment is an R package that includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.
Improves the sensitivity and efficiency of Single-Cell RNA-Barconding and Sequencing (SCRB-seq). mcSCRB-seq is a highly flexible, fast and efficient library protocol with low set-up costs and hence can be a valuable methodological addition for many laboratories.
Assist users in processing various types of sequencing data. Pipeliner is a framework for the definition of sequencing data processing pipelines that are platform independent, fully reproducible, and inherit automated job parallelization and failure recovery. This application was used to create several pipelines for sequencing data processing including bulk RNA-seq, single-cell RNA-seq (scRNA-seq), as well as Digital Gene Expression (DGE) data.