easyRNASeq

easyRNASeq processes high-throughput short-read RNA-Seq data in R/Bioconductor to calculate coverage against a reference genome and summarize counts per exons, genes, or transcripts for gene expression analysis.

Key Features:

• Bioconductor integration: Coordinates Bioconductor packages including ShortRead and Rsamtools for data loading and DESeq and edgeR for downstream analysis.
• Coverage calculation: Calculates coverage of high-throughput short-reads against a reference genome and summarizes this information per feature such as exons, genes, or transcripts.
• Normalization options: Supports RPKM (Reads Per Kilobase Million) and normalization methods provided by DESeq and edgeR.
• Differential expression: Interfaces with DESeq and edgeR for differential gene expression analysis.
• Implementation: Implemented as an R package within the Bioconductor ecosystem.

Scientific Applications:

• Gene expression profiling: Quantifies gene-level expression by summarizing read coverage per gene.
• Transcriptomics: Summarizes coverage and counts at transcript and exon levels for transcriptome analysis.
• Functional genomics: Provides expression quantification to support functional genomics studies.
• Medical and biotechnological research: Supports applied studies requiring differential expression and expression quantification in medicine and biotechnology.

Methodology:

Implemented in R, the package uses ShortRead and Rsamtools for data loading, computes read coverage against a reference genome, summarizes counts per exons/genes/transcripts, and applies normalization (RPKM, DESeq, edgeR) and differential expression analysis via DESeq and edgeR.