nanostring

nanostring performs automated, reproducible, and scalable processing and analysis of NanoString nCounter data for targeted quantification of gene expression across up to approximately 800 genes.

Key Features:

• Comprehensive analysis workflow: Includes quality control, data normalization, expression visualization, annotation with additional metadata, and preparation of input files for differential gene expression analysis.
• Batch processing: Processes multiple samples consistently to support high-throughput analyses.
• Reproducibility and scalability: Implemented as a Nextflow pipeline to enable reproducible and scalable execution across computing infrastructures.
• Portability and environment support: Supports Docker, Singularity, Podman, and Conda environments for deployment across diverse platforms.
• Open-source extensibility: Distributed as open-source code permitting extension and customization.
• Quality metrics reporting: Generates detailed quality metrics for all stages of the analysis.

Scientific Applications:

• Targeted gene expression profiling with NanoString nCounter: Quantification and analysis of expression for up to approximately 800 genes from nCounter assay data.
• Differential gene expression analysis: Produces normalized and annotated inputs suitable for downstream differential gene expression workflows.

Methodology:

Performs quality control, data normalization, expression visualization, annotation with additional metadata, and preparation of input files for differential gene expression analysis; implemented in the Nextflow workflow language and supports Docker, Singularity, Podman, and Conda.