seqpac

seqpac provides comprehensive processing, sequence-based counting, annotation, and group-based analysis of small RNA sequencing (sRNA-seq) data — including microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), transfer RNA fragments (tRFs), and ribosomal RNA fragments (rRFs) — within the R environment.

Key Features:

• Integrated R workflow: Performs end-to-end sRNA-seq processing within R, including adaptor/fastq trimming, counting, annotation, and visualization.
• PAC object framework: Uses a standardized PAC object with three tables: sample phenotypic information (P), sequence annotations (A), and a counts table of unique sequences across experiments (C).
• Sequence-based counting: Preserves raw fastq sequences for counting to maintain sequence integrity and enable detection of sequence-specific biases and novel fragments.
• Group-based summarization and targeting: Summarizes and visualizes sequence counts across sample groups and classifications to identify patterns and relationships.
• Validated trimming performance: Implements fastq trimming whose performance has been validated to be comparable to standard non-R trimming software.

Scientific Applications:

• Class-specific sRNA analyses: Supports analysis of multiple sRNA classes including miRNAs, piRNAs, tRFs, and rRFs.
• Reanalysis of published datasets: Enables reanalysis of existing sRNA-seq datasets to reveal previously unreported biases and sequence features.
• Discovery of novel regulatory fragments: Has been used to identify a novel rRF that is differentially regulated under RNA polymerase I inhibition and up-regulated in tumor-positive patient samples.

Methodology:

Explicit methods stated include fastq/adaptor trimming, sequence-based counting that preserves raw fastq sequences, organization into PAC tables (P, A, C), and group-based summarization and visualization of sequence counts.