IsoEM2

IsoEM2 estimates transcript- and gene-level expression from RNA-Seq data using FPKM and TPM and produces bootstrap samples for confidence intervals that can be used by IsoDE2 for differential expression analysis.

Key Features:

• Expression Level Estimation (IsoEM2): Estimates expression levels in FPKM and TPM for genes and transcripts from RNA-Seq data and reports associated confidence intervals.
• Differential Expression Analysis (IsoDE2): Performs differential expression analysis using bootstrap samples produced by IsoEM2 to identify genes or isoforms with significant expression changes.

Scientific Applications:

• Gene Expression Profiling: To quantify gene- and isoform-level expression across tissues, developmental stages, or experimental conditions using RNA-Seq.
• Disease Research: To identify biomarkers and molecular changes by comparing healthy and diseased samples at gene and isoform resolution.
• Transcriptomics Studies: To investigate alternative splicing and isoform-specific expression changes.

Methodology:

IsoEM2 computes FPKM and TPM expression estimates and applies bootstrapping to generate confidence intervals, and IsoDE2 uses those bootstrap samples to perform differential expression analysis.