rQuant.web

rQuant.web applies quadratic programming to quantify transcript abundances from RNA sequencing (RNA-seq) data while accounting for biases introduced during library preparation, sequencing, and read mapping.

Key Features:

• Quadratic programming-based estimation: Uses quadratic programming to compute transcript abundance estimates from RNA-seq data.
• Bias modeling: Explicitly models and compensates for biases introduced by library preparation, sequencing, and read mapping.
• Multi-transcript resolution: Resolves multiple transcripts per gene locus to enable isoform-level quantification.
• Isoform quantification: Produces quantitative estimates for different RNA isoforms to support analyses of transcript diversity.
• Galaxy integration: Provided as a tool integrated within the Galaxy platform.

Scientific Applications:

• Gene expression studies: Quantifies gene- and transcript-level expression from RNA-seq data.
• Alternative splicing analysis: Distinguishes and quantifies multiple transcripts per locus to support alternative splicing investigations.
• Transcriptional regulation investigation: Supports studies of transcriptional regulation by providing accurate isoform-level abundance estimates.

Methodology:

Applies quadratic programming to estimate transcript abundances while explicitly modeling biases from library preparation, sequencing, and read mapping.