cummeRbund

cummeRbund visualizes and analyzes Cufflinks-generated RNA-seq data to explore gene- and transcript-level expression, differential expression, and splice variants.

Key Features:

• Persistent Storage and Access: Stores and provides access to Cufflinks-generated results for downstream analysis.
• Data Exploration and Manipulation: Enables exploration and manipulation of gene expression patterns and identified splice variants at gene and transcript levels.
• Comprehensive Visualization Functions: Supplies plotting functions for differential expression plots, coverage tracks, transcript abundance graphs, and publication-quality figures.

Scientific Applications:

• Gene Discovery: Supports identification of novel genes and splice variants from RNA-seq/Cufflinks output.
• Comparative Expression Analysis: Facilitates comparison of gene and transcript expression across conditions or experimental setups.
• Differential Expression Reporting: Produces detailed lists of differentially expressed and regulated genes and transcripts.
• Integration with Upstream Tools: Complements TopHat and Cufflinks outputs for downstream visualization and interpretation.

Methodology:

Processes Cufflinks-generated data starting from raw sequencing reads through steps to produce a transcriptome assembly and generates visualizations using scalable, mathematically rigorous analysis.