macpie

macpie streamlines the analysis of high-throughput transcriptomic data from plate-based screens, built on the tidySeurat framework.

Key Features:

• Statistical frameworks: The package incorporates multiple statistical frameworks for data analysis.
• Parallelization: The package leverages parallelization for scalability.
• Preprocessing and quality control: macpie streamlines preprocessing and quality control steps in the analytical pipeline.
• Pathway enrichment: macpie supports pathway enrichment analysis.
• Chemical feature extraction: macpie enables chemical feature extraction from transcriptomic data.
• Multimodal data integration: macpie supports integration across modalities.

Scientific Applications:

• High-throughput transcriptomic profiling: macpie enables scalable characterisation of transcriptional responses to chemical and genetic perturbations using plate-based technologies including MAC-Seq, TempO-seq and PLATE-seq.
• Transcriptome-wide screening: macpie supports reproducible analysis for transcriptome-wide screening applications.

Methodology:

Built on the tidySeurat framework. Leverages Docker and Nextflow. Companion Nextflow pipeline for preprocessing from FASTQ files available separately as dinoflow.