cellHTS2

cellHTS2 performs analysis of high-throughput assays conducted in microtitre plate formats, providing data import, normalization, quality assessment, replicate summarization, statistical scoring, graphical summaries, and transcriptome-based filtering to support RNAi screening and gene-discovery applications.

Key Features:

• Data import and management: Imports and organizes plate-based screening data for downstream analysis.
• Normalization: Applies normalization procedures to adjust plate and technical biases.
• Quality assessment: Performs quality-control analyses to evaluate assay and plate performance.
• Replicate summarization: Summarizes replicate measurements to produce per-well and per-reagent statistics.
• Statistical scoring: Computes statistical scores for hits and assay signals within plate-based screens.
• Graphical summaries: Generates graphical overviews of raw data and analytical results.
• Transcriptome-based filtering: Leverages cell transcriptome information to filter inconsistent outcomes and reduce false positives and negatives.
• Multi-reagent disambiguation: Supports use of multiple independent RNAi reagents per gene to disambiguate inconsistent reagent-level results.

Scientific Applications:

• RNAi screening: Analysis and scoring of RNA interference (RNAi) high-throughput screens for hit identification.
• Gene discovery: Identification of candidate genes from genome-wide or targeted screens using RNAi reagents.
• Cross-species screens: Applied to RNAi screenings in Drosophila cells, human cells, and yeast libraries.

Methodology:

Computational steps explicitly include data import and management, normalization, quality assessment, replicate summarization, statistical scoring, generation of graphical summaries, transcriptome-based filtering of results, and disambiguation using multiple independent RNAi reagents per gene.