modulator v1.0.0 Initial stable release of a Snakemake pipeline for transcript-resolved RNA modification analysis from Nanopore direct RNA sequencing data. Highlights Transcript-resolved analysis via ZN (index) and ZT (identity) partitioning Read-backed transcript assembly with TES/APA clustering Integrated modkit-based modification calling Scalable aggregation with disk-backed external sorting (OOM-safe) Built-in site-level statistical testing (Fisher / chi-square + FDR) Multigene read filtering to remove ambiguous assignments Per-sample QC metrics and transcript-level summaries Pipeline Components Assembly: Isoform reconstruction and annotation (GTF + tagged BAMs) Filtering: Removal of multi-gene overlapping reads Mod calling: Per-transcript modification detection via modkit Aggregation: Long tables and gene/mod pivot summaries Testing: Differential stoichiometry across transcripts Outputs GTF annotation ZT/ZN-tagged BAMs Long and pivot TSV tables Per-transcript metrics and QC summaries Site-level differential testing results Notes Site filtering retains all rows at sites where any row passes thresholds Designed for large-scale datasets with reproducible, parameterized workflows