transcriptR

transcriptR identifies and quantifies de novo continuous regions of transcription across genomes using ChIP-seq histone modification signals to delineate active Transcription Start Sites (TSSs).

Key Features:

• De Novo Identification: Identifies continuous regions of transcription without reliance on prior gene annotations.
• Quantification of Transcription Units: Quantifies transcriptional activity for each identified transcriptional unit.
• Utilization of ChIP-seq Data: Leverages histone modification signals from ChIP-seq experiments to locate active TSSs and inform unit boundaries.
• Interoperability with Bioconductor: Implemented in R for integration with Bioconductor data structures and workflows.

Scientific Applications:

• Characterizing Novel Transcripts: Enables discovery and analysis of previously unannotated genes and non-coding RNAs by defining transcriptional units de novo.
• Studying Gene Regulation: Supports investigation of regulatory mechanisms by mapping active TSSs and associated transcriptional activity.
• Comparative Genomics: Facilitates comparison of transcriptional landscapes across species or experimental conditions using ChIP-seq–based unit definitions.

Methodology:

Uses ChIP-seq datasets to map histone modifications associated with active TSSs and segments the genome into distinct transcriptional units; implemented as an R/Bioconductor package.